The BLAST programs (12–14) perform sequence-similarity searches against a variety of nucleotide and protein databases, returning a set of gapped alignments with links to full sequence records as well as to related transcript clusters (UniGene), annotated gene loci (Gene), 3D structures [Molecular Modeling Database (MMDB)] or microarray studies [Gene Expression Omnibus (GEO)]. The NCBI web interface for BLAST allows users to assign titles to searches, to review recent search results and to save parameter sets in MyNCBI for future use. The basic BLAST programs are also available as standalone command line programs, as network clients and as a local web server package at ftp.ncbi.nih.gov/blast/executables/LATEST/ (Table 2). Table 2.Selected NCBI software available for downloadSoftwareAvailable binariesCategory within this articleBLAST (stand alone)Win, Mac, LINUX, SolarisBLASTBLAST (network client)Win, Mac, LINUX, SolarisBLASTBLAST (web server)Mac, LINUX, SolarisBLASTCD-TreeWin, MacMolecular Structure and ProteomicsCn3DWin, Mac, LINUX, SolarisMolecular Structure and ProteomicsPC3DWin, Mac, LINUXRecent Developmentse-PCRWin, LINUXGenes and Associated Sequencesgene2xmlWin, Mac, LINUX, SolarisGenes and Associated SequencesOMSSAWin, Mac, LINUXMolecular Structure and ProteomicssplignLINUX, SolarisGenes and Associated Sequencestbl2asnWin, Mac, LINUX, SolarisGenomes
