Using MouseBLAST - Available BLAST Programs

This MouseBLAST Help document contains the following information:

• Which BLAST programs can I use with MouseBLAST?
• What's the history of BLAST?
• Where can I get additional information?
• References

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Which BLAST programs can I use with MouseBLAST?

You can use five different programs from the WU-BLAST version 2.0 package in MGI MouseBLAST. WU-BLAST, developed by Warren Gish at Washington University, is an implementation of the BLAST (Basic Local Alignment Search Tool) algorithm by Altschul et al., 1990.

Program	Comparison
BLASTN	Nucleotide query sequence against nucleotide sequence database.
BLASTX	Nucleotide query sequence translated in all reading frames against a protein sequence database. You can use this option to find potential translation products of an unknown nucleotide sequence.
TBLASTX	Six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
BLASTP	Amino acid query sequence against a protein sequence database.
TBLASTN	Protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

What's the history of BLAST?

The Basic Local Alignment Search Tool (BLAST) was first published by Stephen Altschul, Warren Gish, Webb Miller, Eugene Myers, and David Lipman¹ in 1990 from the NCBI. After September 1994, Warren Gish at Washington University started to release enhanced versions of BLAST, WU-BLAST (then at version 1.4). Until that time, there was a single source for BLAST at the NCBI (also at version 1.4).

• WU-BLAST
  Warren Gish also optimized the BLAST programs for speed on different platforms. The first version of WU-BLAST was released in September 1994; in 1996, he released the first "gapped" version of BLAST, WU-BLAST 2.0 (Gish, unpublished). This version allows for gapped alignments and statistics. It can also identify multiple regions of similarity for each sequence match. See http://blast.wustl.edu for details.


• NCBI BLAST
  NCBI was the only source for BLAST when WU-BLAST version 1.4 appeared. In September 1997, (Altschul et al.² released a "gapped" version of BLAST called NCBI BLAST version 2.0. This version included speed enhancements.


• PSI-BLAST
  Altschul et al.² also introduced PSI-BLAST (Position Specific Iterated BLAST) in September 1997 for detecting very distant regions of similarity by running BLAST iteratively. The significant alignments are then used to construct a position-specific score matrix that is used to search the same database again.


• PHI-BLAST
  Zhang et al.³ introduced PHI-BLAST (Pattern Hit Initiated BLAST) in 1998. PHI-BLAST lets you search for protein motifs in sequence databases and is used in conjunction with PSI-BLAST. PHI-BLAST combines regular expression matches with local alignments, and thus, you can find sequences containing a certain pattern with similarity to a particular sequence.

Where can I find additional information?

The NCBI provides BLAST FAQs and a course on the Statistics of Sequence Similarity Scores. Additional BLAST resources are available at the NCBI BLAST site.

References

1. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J. Mol. Biol. (1990), 215(3), 403-10.
2. 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(17), 3389-402.
3. Zhang, Z, Schaffer, AA, Miller, W, Madden, TL, Lipman, DJ, Koonin, EV, Altschul, SF. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. (1998), 26(17), 3986-90.

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