This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.
http://www.ebi.ac.uk/2can/databases/index.html

5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA structure and RNA-protein interactions.
The purpose of this database is to provide information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments.
http://biobases.ibch.poznan.pl/5SData/

AceDB is a genome database designed specifically for handling bioinformatic data flexibly.
http://www.acedb.org/

AceView offers an integrated view of the human and nematode genes as reconstructed by alignment of all publicly available mRNAs and ESTs on the genome sequence.
http://www.ncbi.nlm.nih.gov/AceView/

Prokaryotic Mobile Genetic Elements (MGE's) are central players in mobilizing genes, whether within a given genome (intra-cellular mobility) or between bacterial cells (inter-cellular mobility). Traditionally, MGE's have been classified as either bacteriophages, plasmids or transposons. This classification becomes more and more obsolete as many chimerical elements are identified, which display strong similarities with elements of different families.
We propose therefore ACLAME, a database dedicated to the collection and classification of MGEs from various sources, comprising all known phage genomes, plasmids and transposons.
http://aclame.ulb.ac.be

Dtabase about adrenoleukodystrophy, a progressive, genetic disorder, which affects the adrenal glands and the white matter of the nervous system.
http://www.esid.org/

AEDB is a manual generated database for human alternative exons and their properties - the data is gathered from literature where these exons have been experimentally verified.
http://www.ebi.ac.uk/asd/aedb/index.html

Database about of genetic disorders found in Arab populations.
http://www.agddb.org/

Alport Syndrome is a progressive renal disease with cochlear and ocular involvement. The most common form (~80%) is inherited in an X-linked pattern. X-linked Alport Syndrome (OMIM #301050) is caused by mutations in the type IV collagen alpha chain 5 (COL4A5). The aim of this database is to record all known variants in the COL4A5 gene and their clinical significance. The GenBank sequence NC_000023.9 is used as the reference sequence. The Human Genome Variation Society nomenclature has been used to describe COL4A5 mutations, as well as original nomenclature described by Zhou et al (1994), which includes 202 nucleotides of 5' UTR. ARUP offers full gene sequencing analysis (test 0051786) for classic X-linked Alport syndrome (80% of mutations) and targeted testing for p.C1564S (c.4692G>A), p.L1649R (c.4946T>G), p.R1677Q (c.5232G>A) mutations for adult type Alport syndrome (test 0051710).
http://www.arup.utah.edu/database/ALPORT/ALPORT_welcome.php

AltExtron is a computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns. The alternative events have been delineated and annotated with various characterizations.
http://www.ebi.ac.uk/asd/altextron/index.html

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations.
http://www.ebi.ac.uk/asd/altsplice/index.html

This list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules.
http://www.expasy.org/alinks.html

Constitutional mutations in the androgen receptor gene (AR) impair androgen - dependent male sexual differentiation to various degrees. Somatic mutations in the AR have been found in metastatic prostate cancer. Severe constitutional androgen insensitivity (AI) yields an external female phenotype. Partial constitutional AI yields a range of external genital phenotypes that vary from near - normal female to normal or near - normal male, with or without gynecomastia and other relatively "mild" signs of undervirilization. Some have suggested that clinical severity of AI be divided into three degrees: complete, partial, (when there is appreciable external genital ambiguity) and mild (for the least severe forms). Others have graded severity into seven degrees . The current version of the AR mutation database retains the complete / partial bifurcation of the original database, but provides additional information on the external genitalia and on sex - of - rearing. When external genital ambiguity is appreciable, the sex - of -rearing implies that the external genitalia were predominately male or female. Because different clinical degrees of AI are sometimes seen within families or between those with the same mutation, the new version of the database has an entry for family history.
http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-page+LibInfo+-id+4Flds1F1PA4+-lib+ANDROGENR

Database about the nematode Pristionchus pacificus, created by the University Tuebingen, Germany.
http://appadb.eb.tuebingen.mpg.de

Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms. These novel molecules have many potential uses in medicine and technology.
The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection.
http://aptamer.icmb.utexas.edu/

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenuous agents such as microbes, inflammatory and environmental stimuli.
http://rc.kfshrc.edu.sa/ared/

MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis. By far the most important model systems in cancer research are mammalian organisms. Argonaute compiles comprehensive information on mammalian miRNAs, their origin and regulated target genes in an exhaustive database.
http://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface/

Autosomal Recessive Polycystic Kidney Disease (ARPKD) or Polycystic Kidney and Hepatic Disease 1 (PKHD1) is an important cause of childhood renal- and liver-related morbidity and mortality with a proposed incidence of 1:20,000 - 1:40,000 live births.
This Database lists the mutations and polymorphisms of PKHD1.
http://www.humgen.rwth-aachen.de/

ArrayExpress is a public database of gene expression experiments. These experiments consist of multiple parts (or objects), in order to simplify querying we have provided a query interface which allows you to retrieve the most useful information relating to each experiment, the array(s) and the protocols(s) used.
http://www.ebi.ac.uk/arrayexpress/

After transcription of a gene, the resulting pre-mRNA is spliced before exiting the nucleus. Alternative splicing of a single pre-mRNA can give rise to different mRNA transcripts. Consequently, alternative splicing is an important mechanism for generating protein diversity from a single gene.
http://www.bioinformatics.ucla.edu/ASAP/

Alternative splicing database at EBI; it includes three databases:

ASG is a web-based splicing graph database that integrates transcript information from Ensembl, RefSeq, STACK, TIGR gene index, and UniGene, in order to explore and visualize gene structure and alternative splicing and to provide an exhaustive transcript catalog.
http://statgen.ncsu.edu/asg/

Database about alternataive splicing.
http://sege.ntu.edu.sg/wester/ashes/

The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases.
http://atlasgeneticsoncology.org/

Database of chromosomal breakpoints and other genomic features related to autism, provided by the canadian Centre for Applied Genomics and The Hospital for Sick Children in Toronto.
http://projects.tcag.ca/autism/

Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The database was developed at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg.
http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm

Database about transcriptional regulators of AraC and TetR families.
http://www.bactregulators.org/

Database about genes relevant to cardiovascular and pulmonary disease.
The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. Each cell line contains an insertional mutation in a specific gene.
http://baygenomics.ucsf.edu/

Graphical display of pathways.
http://www.biocarta.com

The BioCatalog is a software directory of general interest in molecular biology and genetics.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4vS+-lib+BIOCATAL

BioConductor is an open source and open development software project for the analysis and comprehension of genomic data.
http://www.bioconductor.org/

International database of tetrahydrobiopterin deficiencies (BIODEF)
Database of mutations causing tetrahydrobiopterin deficiencies (BIOMDEB).
http://www.bh4.org/biomdb1.html

Bipad is a C++ program for predicting one-block or bipartite motifs/patterns shared by a set of nucleotide sequences. This tool, which is particularly useful for transcription factor binding site recognition, was developed by Chengpeng Bi and P.K. Rogan, Laboratory of Human Molecular Genetics, Children's Mercy Hospital and Clinics, 01 Gillham, Kansas City MO 64108
http://bipad.cmh.edu/

Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and evolutionary information can be inferred from well designed queries and alignments. BLAST (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
http://www.ncbi.nlm.nih.gov/BLAST/

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
BLAT was written by Jim Kent. Like most of Jim's software interactive use on this web server is free to all. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. Contact Jim for details.
http://genome.ucsc.edu/cgi-bin/hgBlat

BMRB is a repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids.
http://www.bmrb.wisc.edu/

BodyMap is a database of expression information of human and mouse genes in various tissues or cell types and various timings.
http://bodymap.ims.u-tokyo.ac.jp/doc/bodymapping.html

BRAGI is an interactive protein modeling program. It was developed for the special purpose to model unknown proteins from the structure of a known one. BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. One can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs. BRAGI includes also a set of programs and utility functions.
http://bragi.gbf.de/

BRITE is a database of binary relations for network computation and logical reasoning involving genes, proteins, and other biological molecules.
http://www.genome.ad.jp/brite/

This database contains information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data.
http://www.angis.org.au/Databases/Heart/heartbreak.html

CarpeDB is a epilepsy genetics database. It profiles some 400 genes linked to epilepsy in humans, mice, nematodes, and other organisms.
http://www.carpedb.ua.edu/

The Catalogue of Life is indexing the world's known species.
http://annual.sp2000.org/

Database of sequenced bacterial genomes.
http://www.cbs.dtu.dk/services/GenomeAtlas/

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality.
http://www.ncbi.nlm.nih.gov/projects/CCDS/

CellCircuits is a database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways.
http://www.cellcircuits.org

The Cancer Genome Anatomy Project (CGAP) is an interdisciplinary program established and administered by the National Cancer Institute (NCI) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
http://www.ncbi.nlm.nih.gov/CGAP/

The Candida Genome Database is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data.
http://www.candidagenome.org

CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
http://www.cleanex.isb-sib.ch/

Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages.
http://www.ncbi.nlm.nih.gov/COG/

This database aims to record all published accounts of mutations in the genes encoding human collagen types I and III. Mutations of these collagen types result predominantly in osteogenesis imperfecta and Ehlers-Danlos syndrome type IV respectively.
http://www.le.ac.uk/genetics/collagen/

CORG stands for COmparative Regulatory Genomics. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements.
http://corg.molgen.mpg.de/

COSMIC (Catalogue of Somatic Mutations in Cancer; http://www.sanger.ac.uk/cosmic) is a comprehensive resource that aims to curate the world's literature on somatic mutations in known cancer genes. The catalog includes full and up-to-date curation of mutation data in over 60 well known point-mutated genes, together with novel gene fusion products expressed across genome rearrangement breakpoints, and all of the somatic mutation data from candidate gene screens at the UK's Cancer Genome Project.
http://www.sanger.ac.uk/cosmic

UHN Microarray Centre's CpG Island Database. Here you will find all the information you need to get started with analysing your results from experiments performed on our HCGI 12K and HCGI 8.1K Microarray chip.
http://data.microarrays.ca/cpg/

In mammalian cells, an elevation in the cytosolic cAMP level stimulates the expression of many genes. All genes regulated by cAMP contain a cis-acting DNA sequence, called cAMP-response element (CRE), which binds the phosphorylated form of a transcription factor called CRE-binding (CREB) protein. Researchers can find out which genes the influential protein activates at the CREB Target Gene Database from Marc Montminy of the Salk Institute in La Jolla, California, and colleagues.
http://natural.salk.edu/CREB/

Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site. CUTG was originally developed by Prof. Toshimichi Ikemura at Laboratory of Evolutionary Genetics, National Institute of Genetics. Codon Usage Database is developed and mainteined by Yasukazu Nakamura at The First Laboratory for Plant Gene Research, Kazusa DNA Research Institute.
http://www.kazusa.or.jp/codon/

This database is devoted to the collection of mutations in the CFTR gene and is currently maintained by the laboratory of Lap-Chee Tsui on behalf of the international Cystic Fibrosis genetics research community. It was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers. The specific aim of the database is to provide CF researchers and other related professionals with up to date information about individual mutations in the CFTR gene.
http://www.genet.sickkids.on.ca/cftr/

DBD is a database of predicted transcription factors in genomes based on domain assignments from the SUPERFAMILY and PFAM hidden Markov model libraries. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families.
http://www.transcriptionfactor.org/

dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
http://www.ncbi.nlm.nih.gov/dbEST/index.html

The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.
http://www.ncbi.nlm.nih.gov/gap

DBGET is a simple database retrieval system for a diverse range of molecular biology databases.
http://www.genome.ad.jp/dbget/dbget.links.html

The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA).
http://www.ncbi.nlm.nih.gov/dbGSS/index.html

The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC).
http://www.ncbi.nlm.nih.gov/mhc/MHC.cgi?cmd=init

The Database for Preterm Birth (dbPTB) is a web-based aggregation tool to organize the genes, genetic variations and pathways involved in preterm birth, dbPTB. We used semantic data mining to extract all published articles related to preterm birth. All articles were reviewed by a team of curators. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature.
http://ptbdb.cs.brown.edu/dbPTBv1.php

dbQSNP is a database, that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones.
http://qsnp.gen.kyushu-u.ac.jp/

dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs), in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. dbRIP contains all currently known Alu, L1, and SVA polymorphic insertion loci in the human genome.
http://dbrip.brocku.ca/

A key aspect of research in genetics is associating sequence variations with heritable phenotypes. The most common variations are single nucleotide polymorphisms (SNPs), which occur approximately once every 100 to 300 bases. Because SNPs are expected to facilitate large-scale association genetics studies, there has recently been great interest in SNP discovery and detection.
In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
http://www.ncbi.nlm.nih.gov/SNP/

The STS division file contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites.
http://www.ncbi.nlm.nih.gov/dbSTS/index.html

Based on 400,225 and 580,209 human and mouse full-length cDNA sequences, DBTSS contains exact information of the genomic positions of the transcriptional start sites and the adjacent promoters for 8,793 and 6,875 human and mouse genes, respectively. Of these, 3,324 could be paired as mutually homologous genes between human and mouse and their promoters could be compared with each other.
http://dbtss.hgc.jp

dbZACH is a toxicogenomic information management system, built on a relational database and Java technology, used to store a variety of data generated or otherwise relevant to the Zacharewski lab. The goal of the project is to create a local data management product that is capable of serving the needs of small toxicology laboratories.
http://dbzach.fst.msu.edu/

DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG) with the endorsement of the Ministry of Education, Science, Sport and Culture. From the beginning, DDBJ has been functioning as one of the International DNA Databases, including EBI (European Bioinformatics Institute; responsible for the EMBL database) in Europe and NCBI (National Center for Biotechnology Information; responsible for GenBank database) in the USA as the two other members.
http://www.ddbj.nig.ac.jp

Gene mutation database about deafness, provided by the Harvard Medical School, Center for Hereditary Deafness.
http://hearing.harvard.edu/db/genelist.htm

Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell.
http://tubic.tju.edu.cn/deg/

In order to interpret the molecular basis of the translational process, it is essential to have a corresponding knowledge of the higher structure of the ribosome. A large amount of biochemical data about structure of the ribosome is available at present. Ribosomal cross-linking is one of the most important methods which allows us to get such data.
http://ribosome.ru/

The purpose of this database is to provide an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation. All of the movies are available through the internet.
Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures.
http://projects.villa-bosch.de/dbase/dsmm/

The E-MSD macromolecular structure relational database is designed to be a single access point for protein and nucleic acid structures and related information.
http://www.ebi.ac.uk/msd/index.html

EBI’s (European Bioinformatics Institute's) collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes.
http://www.ebi.ac.uk/genomes/

ECARUCA is a database which collects and provides cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications.
http://www.ecaruca.net/

ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration.
http://genome.ewha.ac.kr/ECgene/

The Eukaryotic Gene Orthologs (EGO), is a database for orthologous genes in eukaryotes.
http://www.tigr.org/tdb/tgi/ego/

Datbase of protein-coding intron-containing genes.
http://www.utoledo.edu/med/depts/bioinfo/database.html

The Edinburgh Mouse Atlas consists of a digital atlas of mouse embryo development and spatially-mapped gene expression.
http://genex.hgu.mrc.ac.uk/

Molecular Databases, accessible by EMBL:
EMBL, EMBLNEW, EMBLGSS, EMBLGSSNEW, SWISSPROT, SWISSNEW, PIR, NRL3D, IMGT, NRSUB, PROSITE, PROSITEDOC, BLOCKS, PRINTS, PFAMA, PFAMB, SWISSPFAM, PFAMSEED, ENZYME, EPD, TFSITE, TFFACTOR, TFCELL, TFCLASS, TFMATRIX, TFGENE, CLUSTALW, PESTFIND, PDB, HSSP, PDBFINDER, MIMMAP, OMIM, REBASE, REBCOMM, SRSFAQ, BIOCAT
http://www.ebi.ac.uk/Information/databases_sitemap.html

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBLRELEASE

EMGLib is a database about the completely sequenced bacterial genomes and the yeast genome.
http://pbil.univ-lyon1.fr/emglib/emglib.html

The ENCODE project aims to discover functional elements in the human genome by intensively annotating 1% of the genome.
http://genome.ucsc.edu/ENCODE/

ENSEMBL is a joint project between EMBL-EBI and the Sanger Center to develop a system which automatically tracks all the sequenced pieces of human genome, attempts to assemble them into large single stretches and then analyse the assembled DNA to find genes and other features of interest to biologists and medical researchers.
http://www.ensembl.org/

Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbNl1KbLgt+-lib+MUSENSEMBL

Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode.>br> Entrez integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

The whole genomes of over 1000 viruses and over 100 microbes can be found in Entrez Genome. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

The Nucleotide database contains sequence data from GenBank, EMBL, and DDBJ, the members of the tripartite, international collaboration of sequence databases. EMBL is the European Molecular Biology Laboratory (EMBL) at Hinxton Hall, UK; DDBJ is the DNA Database of Japan (DDBJ) in Mishima, Japan. Sequences are also incorporated from the Genome Sequence Data Base (GSDB), Santa Fe, NM. Patent sequences are incorporated through arrangements with the U.S. Patent and Trademark Office (USPTO), and via the collaborating international databases from other international patent offices.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

The Structure database or Molecular Modeling DataBase (MMDB) contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from the Protein Data Bank (PDB). The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy.
http://www.ncbi.nlm.nih.gov/Structure/

Genexpression database of the Endocrine Pancreas Consortium.
http://www.cbil.upenn.edu/EPConDB/

The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
http://www.epd.isb-sib.ch

Database about laboratory products used in the epigenetic research field.
http://www.epigenie.com/Epigenetics-Research-Products.html

Compilation of databases and tools on the field of epigenetics.
http://www.epigenie.com/Epigenetics.html

Pox genome database.
http://bio.dfci.harvard.edu/epipox/

The EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. The database ist provided by the Computational Biology and Informatics Laboratory at the University of Pennsylvania.
http://www.cbil.upenn.edu/EpoDB/

The ExInt database incorporates information on exon-intron structure of eukaryotic genes. ExInt accumulates and describes following important characters of the eukaryotic genes: the phases and positions of introns and the exon size and positions of introns for all proteins in GenBank.
http://www.naturalstandard.com/index-abstract.asp?create-abstract=/monographs/genomics/genomic-exint.asp

EXPASy (Expert Protein Analysis System) provides databases for the research on proteomics:
Swiss-Prot and TrEMBL - Protein knowledgebase
PROSITE - Protein families and domains
SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis
ENZYME - Enzyme nomenclature
SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
SWISS-MODEL Repository - Automatically generated protein models
CD40Lbase - CD40 ligand defects
SeqAnalRef - Sequence analysis bibliographic references
http://us.expasy.org/

Tools for the analysis of the human proteom.
http://ca.expasy.org/tools/

Database about the HUS (Haemolytic Uraemic Syndrome); this is a disease associated with microangiopathic haemolytic anemia, thrombocytopenia and acute renal failure. A subgroup of the syndrome is strongly associated with abnormalities within the complement regulator factor H gene.
http://www.fh-hus.org/

FANTOM is a Functional Annotation of Mouse for the RIKEN full-length cDNA clone.
http://fantom2.gsc.riken.go.jp

The Factor H Associated HUS Mutation Database is a database of mutations within the human complement Factor H protein that are associated with Haemolytic Uraemic Syndrome (HUS).
http://www.FH-HUS.org

Flytrap is a database of transposable element insertions in Drosophila melanogaster.
http://www.fly-trap.org/

FlyView is an image database for Drosophila development and genetics, particularly for gene-expression patterns.
http://flyview.uni-muenster.de/

Full Malria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum.
http://fullmal.ims.u-tokyo.ac.jp/

Fungal database, provided by
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850
http://www.tigr.org/tdb/fungal/

GenAge ia a database of genes related to human ageing.
http://genomics.senescence.info/genes/index.html

GenBank is a database of nucleotide sequences from >130,000 organisms. Records that are annotated with coding region (CDS) features also include amino acid translations. GenBank belongs to an international collaboration of sequence databases (described below), which also includes EMBL and DDBJ.
http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
GeneCards is produced by the Weizmann Institute of Science.
http://bioinfo.weizmann.ac.il/cards/

This database is a repository of the genetic variations identified and published in the field of inherited arrhythmogenic diseases and cardiac ion channels.
http://www.fsm.it/cardmoc/

Gene3D is a database of annotated complete genomes.
http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/

Revised and improved annotation of Affymetrix human gene probe sets.
http://genecards.weizmann.ac.il/geneannot/

GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data.
http://research.nhgri.nih.gov/genelink

GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, Genome Database, and mapping resources. GeneLoc is presented by the Weizmann Institute of Science, Rehovot, Israel
http://genecards.weizmann.ac.il/geneloc/

GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers:

GenePaint is a digital atlas of gene expression patterns in the mouse.
http://www.genepaint.org

Genes and Disease is a collection of articles that discuss genes and the diseases that they cause.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd

GeneSeeker is a database for the identification of genes underlying human genetic disorders. This requires the combination of data related to cytogenetic localization, phenotypes and expression patterns, to generate a list of candidate genes.
http://www.cmbi.ru.nl/GeneSeeker/

By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making.
http://www.geneclinics.org/

The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The aim of this database is to identify medically relevant polymorphism from the large volume of polymorphism and mutational data.
http://geneticassociationdb.nih.gov/

Database about deviations from the standard genetic code in various organisms and organelles. Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A.
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

Gene trapping is a high-throughput approach that is used to introduce insertional mutations across the genome in mouse embryonic stem (ES) cells. In addition to generating standard loss-of-function alleles, newer gene trap vectors offer a variety of post-insertional modification strategies for the generation of other experimental alleles. The International Gene Trap Consortium (IGTC) represents all publicly available gene trap cell lines, which are available on a non-collaborative basis for nominal handling fees. Researchers can search and browse the IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways.
http://www.cmhd.ca/sub/genetrap.asp

The goal of the Genome Reviews project is to provide an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes.
http://www.ebi.ac.uk/GenomeReviews/

The first completed genomes from viruses, phages and organelles were deposited into the EMBL Database in the early 1980's. Since then, molecular biology's shift to obtain the complete sequences of as many genomes as possible combined with major developments in sequencing technology resulted in hundreds of complete genome sequences being added to the database, including Archaea, Bacteria and Eukaryota. These web pages give access to a large number of complete genomes.
http://www.ebi.ac.uk/genomes/index.html

GenoMycDB was designed for large-scale comparative analysis, offering a variety of searching/retrieving methods. The selection of aligned pairs with specific attributes can be done based on one or multiple alignment parameters (section Filtering Options, sub-section HSP) – raw score (Score); bit score (Bits); fraction of identical positions for a given HSP (Identity%).
http://www.dbbm.fiocruz.br/GenoMycDB

The Gene Expression Omnibus is a high-throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval. GEO became operational in July 2000.
http://www.ncbi.nlm.nih.gov/geo/

GermOnline is a database that provides access to microarray expression data from experiments relevant for the mitotic and meiotic cell cycle as well as gametogenesis in yeast and higher eukaryotes. In addition to that, GermOnline integrates knowledge about genes important for sexual reproduction.
http://www.germonline.org/

DDBJ’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes.
http://gib.genes.nig.ac.jp

This site provides data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.
http://globin.cse.psu.edu/

Compilation of databases about glycosylation, made by the DKFZ (German Cancer Research Center), Heidelberg.
http://www.dkfz-heidelberg.de/spec2/sweetdb/start.php?action=descriptions

The goal of the Gene OntologyTM (GO) Consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.
http://www.geneontology.org/

The Gene Ontology Annotation (GOA) database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO).
http://www.ebi.ac.uk/GOA/index.html

GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.
http://megasun.bch.umontreal.ca/gobase/gobase.html

Database of completed and ongoing genome projects.
http://www.genomesonline.org/

The GOLD.db was developed to address the need to integrate disparate information on the function and properties of genes and their protein products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders including non-insulin dependent diabetes, various hyperlipidemias, high blood pressure and atherosclerosis.
http://gold.tugraz.at

The Genetic Science Learning Center is an excellent tool for Helping people understand how genetics affects their lives and society.
http://gslc.genetics.utah.edu/

The genome wide association database (GWAS DB) is a repository system and has been constructed to achieve permanent data management and information sharing of genome wide association data. GWAS-DB contains experimental frequency data such as allele frequencies and genotype frequencies, and statistical genetics analysis results such as allelic model, dominant model, recessive model, and additive model and provides graphic viewer to search disease related SNP candidates.
https://gwas.lifesciencedb.jp/cgi-bin/gwasdb/gwas_top.cgi

Gene expression database from the mouse.
http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml

H-Invitational Database (H-InvDB) is a human gene database, with integrative annotation of 41,118 full-length cDNA clones currently available from six high throughput cDNA sequencing projects. This database represents 21,037 cDNA clusters describing their gene structures, functions, novel alternative splicing isoforms, non-coding functional RNAs, functional domains, sub-cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases, gene expression profiling, and comparative results with mouse full-length cDNAs in the context of molecular evolution.
http://www.jbirc.aist.go.jp/hinv/index.jsp

The Database covers the following three main classes of mutant: Point Mutations, Insertions, Deletions
http://hadb.org.uk/WebPages/Database/Quiz/intrquiz.htm

A database of point mutations and short additions and deletions in the factor IX gene.
http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html

The Human Ageing Genomic Resources (HAGR) are a collection of databases and tools designed to help researchers understand the genetics of human ageing. A major resource in HAGR is the core gene database GenAge, a database of genes related to human ageing. Featuring over 2,000 species, AnAge provides a basis for the comparative biology of ageing.
http://genomics.senescence.info/

The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors.
http://www.hapmap.org/index.html.en

Database about human hemoglobin variants and thalassemias.
http://globin.cse.psu.edu/globin/hbvar/

The Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The project comprises two databases:

Database about hepatitis C.
http://hepatitis.ibcp.fr/

Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome.
http://hembase.niddk.nih.gov/

The Hematopoiesis Promoter Database (HemoPDB) has been developed as a information resource focused on transcriptional regulation in hematopoiesis. HemoPDB is composed of integral, experimentally defined regulatory information, including TFs, cis-regulatory elements, their target gene promoters and corresponding annotations, with links to supporting published references. Accordingly, the database may be searched by Gene Symbol, GenBank Accession Number, UniGene ID, TF (binding site) Name and lineage or cell type within which a gene is expressed.
http://bioinformatics.wistar.upenn.edu/HemoPDB/

Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.
http://herv.img.cas.cz

The Human Gene Mutation Database (HGMD) represents an attempt to collate known (published) gene lesions responsible for human inherited disease. This database, whilst originally established for the study of mutational mechanisms in human genes (Cooper and Krawczak 1993), has now acquired a much broader utility in that it embodies an up-to-date and comprehensive reference source to the spectrum of inherited human gene lesions. Thus, HGMD provides information of practical diagnostic importance to (i) researchers and diagnosticians in human molecular genetics, (ii) physicians interested in a particular inherited condition in a given patient or family, and (iii) genetic counsellors.
http://www.hgmd.cf.ac.uk/

The objective of HGVbase (the Human Genome Variation Database) is to provide an accurate, high utility and ultimately fully comprehensive catalog of normal human gene and genome variation, useful as a research tool to help define the genetic component of human phenotypic variation. All records are highly curated and annotated, ensuring maximal utility and data accuracy.
HGVbase is the product of a collaboration between the Karolinska Institute (Sweden), the European Bioinformatics Institute (UK).
http://hgvbase.cgb.ki.se/

List of human genome variation databases. This list was compiled by Rania Horaitis at the Genomic Disorders Research Centre, Melbourne.

The HIV Sequence Database focuses on five primary goals:
Collecting HIV and SIV sequence data (since 1987)
Curating and annotating this data, and making it available to the scientific community
Computer analysis of HIV and related sequences
Production of software for the analysis of (sequence) data
Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.
http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html

The HIV Sequence Database focuses on five primary goals:
Collecting HIV and SIV sequence data (since 1987)
Curating and annotating this data, and making it available to the scientific community
Computer analysis of HIV and related sequences
Production of software for the analysis of (sequence) data
Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.
http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html

HIV Structural Reference Database and Chem-BLAST at NIST Biotechnology Division, National Institute of Standards and Technology Gaithersburg, MD 20899 U.S.A.
http://xpdb.nist.gov/hivsdb/hivsdb.html

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.
http://www.hmdb.ca/

The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases.
http://bioinfo.nist.gov/

Hoppsigen is a nucleic database of homologous processed pseudogenes.
http://pbil.univ-lyon1.fr/databases/hoppsigen.html

Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
The mRNA expression levels of thousands of genes in a collection of normal human organs were obtained using high-density oligonucleotide array technology and deposited in this public database.
http://zlab.bu.edu/HugeSearch/nph-HugeSearch.cgi

Database, produced by the HUGO Gene Nomenclature Committee, providing all the gene symbols.
http://www.genenames.org/index.html

NCBI's Genome Browser.
http://www.ncbi.nlm.nih.gov/genome/guide/human/

HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome.
http://humancyc.org/

The human siRNA database (HuSiDa) is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup and actual procedure of specific RNAi experiments in human cells.
http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm

The HvrBase is a tool for the analysis of human and primate mitochondrial DNA (mtDNA).
http://www.hvrbase.org/

X-linked severe combined immunodeficiency (XSCID or X-SCID) is an immune disorder caused by mutations in the X-linked gene IL2RG, which encodes the common gamma chain (c) of the lymphocyte receptors for interleukin-2 (IL-2) and many other cytokines. A database of human XSCID mutations (IL2RGbase) has been assembled. Information on new mutations may be submitted online.
http://research.nhgri.nih.gov/scid/

The Integrated Microbial Genomes (IMG) system provides a framework for the comparative analysis of the genomes sequenced by the Joint Genome Institute.
http://img.jgi.doe.gov/

The international ImMunoGeneTics information system (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire (LIGM; Universite Montpellier II and CNRS) at Montpellier, France
http://www.ebi.ac.uk/imgt/

IMGT/PRIMER-DB was implemented by Julien Bertrand (LIGM, Montpellier, France) and Géraldine Folch (EUROGENTEC).
http://imgt.cines.fr/IMGTPrimerDB/

Informations about vertebrate immunoglobulin and T cell receptor genes.
http://imgt.cines.fr/cgi-bin/GENElect.jv

Informations about the Familial Mediterranean Fever and hereditary autoinflammatory diseases.
http://fmf.igh.cnrs.fr/infevers/

Integr8 is a browser for information relating to completed genomes and proteomes, based on data contained in Genome Reviews and the UniProt proteome sets. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.
http://www.ebi.ac.uk/integr8/

Database about Drosophila genes and their roles in development.
http://www.sdbonline.org/fly/aimain/1aahome.htm

Database about genes induced by treatment with interferons.
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi

The Intronerator is a collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing.
http://www.cse.ucsc.edu/~kent/intronerator/

Database about intronless genes.
http://sege.ntu.edu.sg/wester/intronless

Database about virally encoded IRESes and cellular mRNA encoded IRESes. It was developed by Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço and Stéphan Vagnerat The French Institute of Health and Medical Research.
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/

The IRESite database contains information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure. The IRESite database contains information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.
http://www.iresite.org/

The Influenza Sequence Database is a curated database of nucleotide sequences. It is intended to provide the research community with easy sequence deposit and retrieval capabilities, together with tools tailored, in particular, to the analysis of hemagglutinin and neuraminidase sequences.
This database is operated by the University of California for the US Department of Energy
http://www.flu.lanl.gov/

Receptor Nomenclature DAtabase by the International Union of Pharmacology (IUPHAR).
http://www.iuphar-db.org/

The Influenza Virus Database (IVDB) integrates information and creates an analysis platform for genetic, genomic, and phylogenetic studies of the virus.
http://influenza.big.ac.cn/

JASPAR is a collection of transcription factor DNA-binding preferences, modelled as position-specific weight matrices (PSSMs).
http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl

Jpo_prt - a library of patented protein sequences from the Japanese Patent Office in the public domain.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbNl1KbLj1+-lib+JPO_PRT

JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister’s Millennium Project. The aim of this undertaking is to identify and collate up to 150.000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence the coding sequence of the genes. The project has been carried out by a collaboration between the Human Genome Center (HGC) in the Institute of Medical Science (IMS) at the University of Tokyo and the Japan Science and Technology Corporation (JST).
http://snp.ims.u-tokyo.ac.jp/

KDBI provides experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature.
http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp

KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks in biological processes (PATHWAY database), the information about the universe of genes and proteins (GENES/SSDB/KO databases), and the information about the universe of chemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases).
http://www.genome.ad.jp/kegg/

KEGG/EXPRESSION is a database system for integrated analysis of gene expression profile data, together with KEGG pathway data and genome sequence data.
http://www.genome.ad.jp/kegg/expression/

The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development.
http://golgi.ana.ed.ac.uk/kidhome.html

KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders.
http://bioinf.uta.fi/KinMutBase/

Database about mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy.
http://projects.tcag.ca/lafora/

Database about genes involved in the pathogenesis of Progressive Myoclonus Epilepsy (PME) of the Lafora type.
http://projects.tcag.ca/lafora/

The Leukemia Gene Atlas (LGA) is a public platform that supports the research and analysis of molecular data of leukemias. In addition to the molecular data the LGA stores the corresponding clinical and laboratory data. The LGA supports comprehensive queries of data, the visualization and analysis as well as download and upload. Currently, there are gene expression, methylation, sequencing data and genotypes of over 6000 samples in the LGA. To analyze data the user may choose between a set of tools: cluster analyses, statistical tests, data distribution plots and the Integrative Genomics Viewer (IGV).
http://www.leukemia-gene-atlas.org/

Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. A database of mutations causing Lowe syndrome has been established. Information on new mutations may be submitted online.
http://research.nhgri.nih.gov/lowe/

Database about the Malaria Transcriptome, provided by the University of California San Francisco.
http://malaria.ucsf.edu/

MAPPER is a platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes.
http://bio.chip.org/mapper

MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly.
http://mbgd.genome.ad.jp/

This database has been developed to facilitate the identification and differentiation of syndromic entities. Special attention is given to the type of information which, because of space the limitations of the printed form, is usually limited or completely omitted in the existing reference sources.
http://www.nlm.nih.gov/archive/20061212/mesh/jablonski/syndrome_toc/toc_a.html

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways from more than 300 different organisms.
http://metacyc.org/

Database of DNA methylation.
http://www.methdb.de

The purpose of this database is to provide the scientific community with a resource to store DNA methylation data and to make these data readily available to the public. Futur development of the database will focus on environmental effects on DNA methylation. It attempts to store all data about DNA methylation in a common source. It can be searched in different ways, ranging from a simple browse mode to detailed queries for sequence-specific DNA methylation profiles and patterns, total methylation content data or environmental conditions that can influence the methylation state of DNA.
http://www.methdb.net/

To study interplay of DNA methylation, gene expression and cancer, a database for human DNA Methylation and Cancer was developed. MethyCancer hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Furthermore, a powerful search tool is developed to provide user-friendly access to all the data and data connections. A graphical MethyView shows DNA methylation in context of genomics and genetics data facilitating the research in cancer to understand genetic and epigenetic mechanisms that make dramatic changes in gene expression of tumor cells.
http://methycancer.psych.ac.cn/

The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. All MGC sequences are deposited in GenBank and the clones can be purchased from distributors of the IMAGE consortium.
http://mgc.nci.nih.gov/

Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/

Micro-Mar is a database for dynamic representation of marine microbial biodiversity.
http://egg.umh.es/micromar/

Guide to microRNA and microRNA Databases.
http://www.micrornadatabase.com/

microRNA.org is a resource for predicted microRNA targets and expression provided by the Memorial Sloan-Kettering Cancer Center.
http://www.microrna.org/microrna/home.do

MiGenes is a relational database of mitochondrial-related gene products. It includes major model organisms such as human, mouse, rat, fruit fly, worm, baker’s yeast and fission yeast.
http://www.pharm.stonybrook.edu/faculty/bogenhagen/lab/migenes.htm

Database of microRNAs (small non-coding RNAs), provided by the Sanger Institute.
http://microrna.sanger.ac.uk/sequences/

The information in the Mitelman Database of Chromosome Aberrations in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman, Bertil Johansson, and Fredrik Mertens.
http://cgap.nci.nih.gov/Chromosomes/Mitelman

This database is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although we are including proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria.
http://www-lecb.ncifcrf.gov/mitoDat/

MITOMAP is a compendium of polymorphisms and mutations of the human mitochondrial DNA.
http://www.mitomap.org/

Database about the mitochondrial proteom.
http://www.mitop.de:8181/mitop2/

Group II introns are a novel class of RNAs best known for their self-splicing reaction. Under certain in vitro conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of protein.
http://www.fp.ucalgary.ca/group2introns/

The Molecular Probe Data Base (MPDB) contains information on ca. 4.300 synthetic oligonucleotides with a sequence of up to 100 nucleotides.
http://www.biotech.ist.unige.it/interlab/mpdb.html

The Human Mitochondrial Genome Database (mtDB) provides a database of complete human mitochondrial genomes.
http://www.genpat.uu.se/mtDB/

The GiiB-JST mtSNP (mitochondrial single nucleotide polymorphism) database provides information related to the functional differences among mitochondrial SNPs. This web site is useful for identification of mtSNPs associated with age-related conditions such as longevity, Parkinson's disease, and Alzheimer's disease, as well as those related to energy metabolism such as obesity, thinness, and type-2 diabetes, or to atherosclerosis.
http://www.giib.or.jp/mtsnp/index_e.html

Diese Website enthält Links zu folgenden Datenbanken:

Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
NUCLEOTIDE DATABASES
dbEST, dbGSS, dbSNP, dbSTS, Nucleotide, GenBank, HomoloGene, MGC, PopSet, RefSeq, TPA, Trace Archive, UniGene, UniSTS
PROTEIN DATABASES
Domains, Proteins, PROW, RefSeq
STRUCTURE DATABASES
Domains, 3D Domains, Structure (MMDB)
TAXONOMY DATABASES
Taxonomy
GENOME DATABASES
Genomes, Gene, LocusLink, COGs
EXPRESSION DATABASES
Geo, Geo Datasets, SAGE
http://www.ncbi.nlm.nih.gov/Database/index.html

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.
http://www.ncbi.nlm.nih.gov/biosystems/

Graphical view of chromosomes of different organisms, including homo sapiens.
http://www.ncbi.nlm.nih.gov/mapview/

The NCBI Map Viewer displays genome assemblies using sets of aligned chromosomal maps. A new Map Viewer home page organizes the available organisms by taxonomic group and provides links to both Map Viewer and Genomic BLAST pages.
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=hum_chr.inf&query#availdoc

The database provides access to all RNA structures in which a particular rare base pair has been found.
http://prion.bchs.uh.edu/bp_type/

The database contains published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.
http://www.ucl.ac.uk/ncl/

The NDB shows nucleic acid-containing structures in a X-ray atlas and in a NMR-atlas.
http://ndbserver.rutgers.edu/

Database about Neisseria meningitidis.
http://pubmlst.org/perl/mlstdbnet/mlstdbnet.pl?file=pub-nm_profiles.xml

Nematode.net is a resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis.
http://nematode.net/

NEMBASE is a database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project.
http://www.nematodes.org

NetAffx details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix.
http://www.affymetrix.com/analysis/index.affx

A taxonomy database, integrating taxonomy data compiled at NCBI and data specific to the Swiss-Prot database.
http://www.ebi.ac.uk/newt/

NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs).
The database contains 5,339 public sequences from 861 organisms covering all kingdoms of life, including vira and viroids. Including 109 traditional classes distributed in 26 cellular process. 1,114 entries is related to disease, is transcribed from repeats or imprinted domains, is induced or repressed by stress, or is specific to a certain species, sex, tissue, or developmental stage, have been included.
http://www.noncode.org/

Database with informations about noncoding RNA.
http://biobases.ibch.poznan.pl/ncRNA/

Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database.
http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+ui2s1Ps6V1+-lib+NUCLEOSOME

Database about genes involved in obesity.
http://obesitygene.pbrc.edu/

The Ovarian Kaleidoscope database (OKdb) is a collaborative online resource for scientists investigating the ovary. It provides information regarding the biological function, expression pattern, and regulation of genes expressed in the ovary, as well as for the phenotypes associated with their mutation.
http://ovary.stanford.edu/

Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM&cmd=Limits

The OMIM Morbid Map presents the cytogenetic map location of disease genes described in OMIM.
http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi?

OMIMALLELE contains alleles (mutations and polymorphisms) reported in OMIM.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+uhTO1RlLQc+-lib+OMIMALLELE

Collection of ORFs that are sold by Invitrogen
http://orf.invitrogen.com/

PAHdb is an locus-specific database for mutations in the human phenylalanine hydroxylase gene (symbol PAH) and the associated phenotypes at the levels of protein, metabolites and organism.
http://www.pahdb.mcgill.ca/

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
http://www.ebi.ac.uk/goldman-srv/pandit/

The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions.
http://www.pantherdb.org/

Parasite - Genome database, produced by the 9712 Medical Center Drive Rockville, MD 20850
http://www.tigr.org/tdb/parasites/

Patent_DNA - a library of patented DNA sequences from the European Patent Office in the public domain.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbNl1KbLkV+-lib+PATENT_DNA

Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are also available.
Produced by the Department of Anatomy, University of Cambridge.
http://www.pathbase.net/

Cell signaling pathways can be conveniently explored using PathFinder, an interactive, online graphical representation of cell signaling pathways.
http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/PathFinder.html

"Pathway", the list of pathway maps is a part of the KEGG system. KEGG (Kyoto Encyclopedia of Genes and Genomes) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by the genome sequencing projects. The KEGG project is being undertaken in the Institute for Chemical Research, Kyoto University as a part of the Japanese Human Genome Program.
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+PATHWAY

Biomolecular interactions and cellular processes assembled into authoritative human signaling pathways.
http://pid.nci.nih.gov/

Database of full-length enriched cDNA libraries and ESTs in pigs.
http://pede.gene.staff.or.jp/

PepHMM is a hidden Markov Model based scoring function for mass spectrometry database search.
http://msms.cmb.usc.edu/PepHMM/PepHMM.htm

Public expression profiling resource provides expression profiles in a variety of diseases and conditions.
http://pepr.cnmcresearch.org/

Database about the Genome of the Malaria causing Plasmodium falciparum.
http://www.tigr.org/tdb/edb2/pfa1/htmls/

PGDB is a database of human genes related to the prostate and prostatic diseases.
http://www.urogene.org/pgdb/

PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene in this database allows the user to compare phenotypes of a gene over many organisms simultaneously.
http://www.phenomicDB.de

Database about nucleotide variation found in the PHEX gene, the majority of which are found in patients with X-linked hypophosphatemia.
http://www.phexdb.mcgill.ca/

Informations about SNPs in cDNA of the pig.
http://pede.gene.staff.or.jp/csnp/csnp_main.php

PlasmoDB is the official database of the malaria parasite genome project. This resource provides access to finished sequence for Plasmodium falciparum (strain 3D7), generated by the Sanger Institute, TIGR/NMRC, and Stanford, in addition to a wide range of related genomic-scale datasets from other sources.
http://plasmodb.org/

PolyA_DB is a database which provides several types of information regarding polyadenylation in mammalian species:

PolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
http://www.bork.embl-heidelberg.de/PolyPhen/

A PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via Sequin, often as a sequence alignment.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Popset

Ribosomal RNA-(rRNA)-targeted oligonucleotide probes are widely used for culture-independent identification of microorganisms in environmental and clinical samples. ProbeBase is a comprehensive database containing more than 700 published rRNA-targeted oligonucleotide probe sequences.
http://131.130.66.201/probebase/

The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks.
http://prodoric.tu-bs.de/

The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks.
http://prodoric.tu-bs.de

PromEC is a database of E. coli mRNA promoters with experimentally identified transcriptional start sites.
http://bioinfo.md.huji.ac.il/marg/promec/

Database about mutations and polymorphisms in the PTCH1 gene.
http://www.cybergene.se/PTCH/ptchbase.html

The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays. All data has been gathered from published articles, cited in PubMed. This resource is a collaborative effort of the NCI-Frederick Gene Expression Laboratory and the CGAP Genome Annotation Initiative.
http://web.ncifcrf.gov/rtp/gel/primerdb/

The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
http://rgd.mcw.edu/

The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
http://rdp.cme.msu.edu/

The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a resource of core pathways and reactions in human biology.
http://www.reactome.org/

The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information.
http://recode.genetics.utah.edu/

The recurrent aberrations were derived from the Mitelman Database of Chromosome Aberrations in Cancer (2003) and include all cytogenetic changes present in at least two cases of the same morphologic entity, and, whenever applicable for solid tumors, within the same site. The complete karyotypes, patient characteristics, and references are found in the Mitelman Database of Chromosome Aberrations in Cancer.
http://cgap.nci.nih.gov/Chromosomes/RecurrentAberrations

Database for gene expression analysis.
http://157.82.78.238/refexa/main_search.jsp

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/

Repbase Update is a database of repetitive elements from diverse eukaryotic organisms.
http://www.girinst.org/Repbase_Update.html

Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/

This database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.
http://www.psb.ugent.be/rRNA/index.html

Database about ribosomal RNA.
http://www.psb.ugent.be/rRNA/index.html

Database about the ribosomal differentiation of medical relevant microorganisms.
http://www.ridom-rdna.de/

Compilation of RNA databases by the Israel Science and Technology Directory.
http://www.science.co.il/biomedical/RNA-Databases.asp

The RNA Modification Database is a comprehensive list of post-transcriptionally modified nucleosides from RNA.
http://library.med.utah.edu/RNAmods/

ROSPath is a database for proteins involved in ROS-mediated signaling pathways.
http://rospath.ewha.ac.kr

RPG is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli.
http://ribosome.miyazaki-med.ac.jp/

Database for real-time PCR primer and probe sequences.
http://medgen.ugent.be/rtprimerdb/

This database includes genes and interventions that have been studied with respect to their effects on life-span or age-related neurological diseases.
http://sageke.sciencemag.org/cgi/genesdb

Satellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia.
http://satellog.bcgsc.ca/

The database includes an initial set of eukaryotic genomic annotations, with special emphasis on the human selenoproteome, for immediate inspection by selenium researchers or incorporation into more general databases.
http://www.selenodb.org/

SIDDBASE is a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes.
http://www.cbs.dtu.dk/ws/ws.php?entry=SIDDbase

Ribosomal RNA database.
http://www.arb-silva.de/

Database about Short interfering RNAs.
http://siRecords.umn.edu/siRecords/

siRNA Database made by the Center for Genomics and Bioinformatics / Karolinska Institute.
http://sirna.cgb.ki.se/

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
http://genome-www5.stanford.edu/

The SNP Consortium Ltd. is a non-profit foundation organized for the purpose of providing public genomic data. Its mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make the information related to these SNPs available to the public without intellectual property restrictions.
http://snp.cshl.org/

The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.
http://snp500cancer.nci.nih.gov/

SNPper (pronounced 'snipper') is a web-based application to look for known Single Nucleotide Polymorphisms (SNPs) in public databases.
http://snpper.chip.org

SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
http://source.stanford.edu/

The rapid accumulation of knowledge on biological signaling pathways and their regulatory mechanisms has highlighted the need for specific repositories that can store, organize and allow retrieval of pathway information in a way that will be useful for the research community. SPIKE is a database for achieving this goal, containing highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction.
http://www.cs.tau.ac.il/~spike/

SpliceDB is a database of known mammalian splice site sequences.
http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb

SpliceNest is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences from GeneNest to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA.
http://splicenest.molgen.mpg.de

More then 300 molecular biology databases
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+databanks+-id+1rbMI1Kc4sq

The Signal Transduction Classification Database (STCDB) is a database about to the classification of signal transduction.
http://bibiserv.techfak.uni-bielefeld.de/stcdb/

While the use of STRs for genetic mapping and identity testing has become widespread among DNA typing laboratories, there is no single place where information may be found regarding STR systems. This web site is an attempt to bring together the abundant literature on the subject in a cohesive fashion to make future work in this field easier. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included in this database. Addresses for scientists and organizations working in this area have also been included as well as a comprehensive reference listing of material on STRs used for DNA typing purposes.
http://www.cstl.nist.gov/div831/strbase/

STRING is a database of known and predicted protein-protein interactions.
http://string.embl.de/

SubViral RNA: a database of the smallest known auto-replicable RNA species.
http://subviral.med.uottawa.ca/

TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA (ref. 1). As an option, nonconserved sites are also predicted.
http://www.targetscan.org/

The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy

Germline mutations of the TBX5 gene were identified as the primary cause in up to 70% of patients with Holt-Oram syndrome (HOS), an autosomal dominant disorder characterized by malformations of the upper limbs and cardiac defects. The database informs about the genetic variations within the TBX5 gene. The databank is maintained by the Institute of Human Genetics, University of Leipzig, Germany.
http://www.uni-leipzig.de/~genetik/TBX5

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health, U.S. Department of Health and Human Services.
http://cancergenome.nih.gov/

TESS is a web tool for predicting transcription factor binding sites in DNA sequences.
http://www.cbil.upenn.edu/tess/

TFExplorer is a database for predicted regulatory elements in human, mouse, and rat. It shows predicted binding sites of transcription factors in the promoter regions, along with their phylogenetic footprinting information. In addition, TFExplorer can search for genes that have a given sequence pattern in their promoter regions using the motif-searching method.
http://mars.kribb.re.kr:8080/tfExplorer/

A TPA sequence is derived or assembled from primary sequence data currently found in the DDBJ/EMBL/GenBank International Nucleotide Sequence Collaboration Databases. It can be genomic or mRNA sequence, and can be assembled or derived from primary genomic and/or mRNA sequences.
http://www.ncbi.nlm.nih.gov/Genbank/TPA.html

Organism-specific databases of EST and gene sequences.
http://www.tigr.org/tdb/tgi/

The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals.
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl

The database contains lists of completed and ongoing genome projects with links to complete genome sequences.
http://www.tigr.org/tdb/mdb/mdbcomplete.html

The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called "10S RNA").
http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html

Database about the geneexpression in tooth.
http://bite-it.helsinki.fi/

This database allows visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations as described in Stitziel et. al. (JMB,327(5):1021-1030).
http://gila.bioengr.uic.edu/snp/toposnp/

TraitMap contains curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana.
TraitMap is the first database of mapping charts in genetics, and it is integrated in a web-based retrieval framework: termed Genome <--> Phenome Superhighway (GPS) system, where it is possible to combine and visualize multiple mapping records in a two-dimensional display.
http://omicspace.riken.jp/gps/

TRANSCompel is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signalling pathways.
http://www.gene-regulation.com/pub/databases.html#transcompel

The TRANSCompel database emphasizes the key role of specific interactions between transcription factors binding to their target sites providing specific features of gene regulation in a particular cellular content.
http://www.gene-regulation.com/pub/databases.html#transcompel

TRANSFAC is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
http://www.gene-regulation.com/pub/databases.html#transfac

TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.
http://www.membranetransport.org/

The Database Of Tandem Repeats In The Human Genome is maintained by the Bioinformatics Centre, Washington Singer Laboratories, University of Exeter, UK.
http://trbase.ex.ac.uk/

Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats.
https://tandem.bu.edu/cgi-bin/trdb/trdb.exe

Transcriptional Regulatory Element Database (TRED) is a repository for both cis- and trans- regulatory elements in mammals.
http://rulai.cshl.edu/tred

The Tree of Life is a collaborative web project, produced by biologists from around the world. On more than 2600 World Wide Web pages, the Tree of Life provides information about the diversity of organisms on Earth, their history, and characteristics.
Each page contains information about one group of organisms (for example, the Coleoptera page gives information about all beetles, the Salticidae page about jumping spiders, the Cephalopoda page about squids, octopi, and related molluscs, and the Fungi page about fungi).
http://tolweb.org/tree/

Database about tRNA, hosted and maintained in a cooperation between the universities of Leipzig (Germany), Marburg (Germany) and Strasbourg (France).
http://trnadb.bioinf.uni-leipzig.de/

TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimental information is included into TRRD.
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/

TrSDB-TranScout Database-(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation.
http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl

Database about the Genome of Mycobacterium tuberculosis.
http://tuberculist.epfl.ch/

Database about human mutations of the turkish population.
http://hmut-tr.sourceforge.net/

UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene

UniSTS is a NCBI resource that reports information about markers, or Sequence Tagged Sites (STS).
For each marker, UniSTS displays the primer sequences, product size, and mapping information, as well as cross references to LocusLink, dbSNP, RHdb, GDB, MGD, and the Entrez Map Viewer. The marker report also lists GenBank and RefSeq records that contain the primer sequences, as determined by Electronic PCR (e-PCR). Marker data, e-PCR and mapping data are availble from the FTP site.
UniSTS integrates marker and mapping data from public resources including GenBank, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists

UniVec is a database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination). Screening using UniVec is efficient because a large number of redundant sub-sequences have been eliminated to create a database that contains only one copy of every unique sequence segment from a large number of vectors.
http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html

VBASE2 is a database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences.
http://www.vbase2.org/

This resource provides access to viral genomes and a variety tools for comparative genomic analyses. At the heart of the system is VOCs (Virus Orthologous Clusters), a database with built-in tools that allows users to retrieve and analyze the genes, gene families, and genomes of 11 different virus families. The database is the source of information for other programs of the workbench for whole genome alignments, genome display, or gene/protein sequence analysis.
http://athena.bioc.uvic.ca/

Characterization and classification of nucleic acid vectors.
http://genome-www.stanford.edu/vectordb/

Database for complete viral genome sequences.
http://115.111.37.206/virgen/virgen.asp

VirOligo is a database of virus-specific oligonucleotides.
http://viroligo.okstate.edu

MOLECULAR AND CELLULAR BIOLOGY LEARNING CENTER The lessons are produced in cooperation between the National Sience Foundation and the U.S. Department of Education.
http://vcell.ndsu.nodak.edu/animations/

VISTA is a program for visualizing global DNA sequence alignments of arbitrary length.
http://www-gsd.lbl.gov/VISTA/

WebQTL stors data about gene expression, neuropharmacological,anatomical, and behavioral data for over 30 strains of mice.
http://www.webqtl.org/

WormBase is the central data repository for information about Caenorhabditis elegans and related nematodes.
http://www.wormbase.org/

WormBase is the central data repository for information about Caenorhabditis elegans and related nematodes.
http://www.wormbase.org/

The ability to identify male-specific DNA renders polymorphic Y-chromosomal sequences an invaluable addition to the standard panel of autosomal loci used in forensic genetics (Roewer 2009). Y-STR haplotyping is particularly important for sensitive typing of male DNA in mixed stains as well as for rapid assortment of biological crime scene evidence. Moreover, Y chromosomal profiling can trace back paternal lineages into the past and has thus been proven a useful tool in genealogical and kinship testing. The individuality of the male-specific part of the Y chromosome can be optimally explored by the Y-STR haplotype analysis using a set of highly variable short tandem repeat markers approved by the forensic and scientific community.
http://www.yhrd.org/