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/

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

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/

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/

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

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

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/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/

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

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