BLAST searches program

Genome BLAST refers to the application of any of the BLAST search programs to the complete genomic sequence of an organism or the transcript and protein sequences derived from its annotation. 

Altschul S F, T L Madden, A A Schaffer, J Zhang, Z Zhang, W Miller and D J Lipman 1997. Gapped BLAST and PSI-BLAST A New Generation of Protein Database Search Programs. Nucleic Acids Research 25 3389-3402. 

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-402. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

A nucleotide or peptide sequence is searched against the EST database using the BLAST (see BLAST server Karlin and Altschul, 1990 and 1993 Altschul et al., 1997) searching programs. 

Altschul, S., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST anmd PSI-BLAST a new generation of protein database search programs. Nucl. Adds Res. 25, 3389-3402. 

S.F. Altschul, T.L. Madden., A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST A new generation of protein database search programs Nucleic Acids Res. 25 3389-3402. (PubMed) (Full Text in PMC)... 

Database search programs like FASTA [18] or BLAST [19] have been optimised to detect evolutionary relationships between proteins, and are readily adequate for template recognition and (multiple) sequence alignment in cases where the sequence identity is over 25-30% [20], The general procedure is to assume next that the backbone of the model is identical to the one of the template structure and add the side chains onto it [21], although some difficulties may arise with insertions, deletions and local low similarity. 

The picture of what a bioinformatician does used to be dominated by the BLAST search. Well, maybe, it is more PSI-BLAST, today. In short, a bioinformatician was envisioned doing turn-key analysis of biological data using a very small set of programs, sometimes even a single program. In recent years bioinformatics has become much more than that and, at the same time, not reached the level of expectation yet with which it is confronted by biologists. 

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