BLAST

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267

Chapter 14

CHAPTER 14

WU-BLAST Reference

WU-BLAST was developed and is maintained entirely by Warren Gish. He was one

of the original authors of BLAST while at the NCBI but is now at Washington Uni-

versity in St. Louis (where the WU comes from). Development began in 1994 at Ver-

sion 1.4, before BLAST had gapped alignments. Quite a lot has changed since then.

Paradoxically, WU-BLAST is more similar to the original BLAST than the current

NCBI version.

WU-BLAST is useful because it has more command-line parameters that allow

advanced users to control the program with more precision. It is also faster.

Table 14-1 displays features unique to WU-BLAST or significantly different from

NCBI-BLAST.

Table 14-1. WU- and NCBI-BLAST feature differences

Feature WU-BLAST NCBI-BLAST

Word size Any word size for any program mode. Neigh-

borhood words are turned off for word sizes

of 5 or greater, but may be activated by set-

ting an explicit value for

T.

blastn has a minimum word size of 7. blastp,

blastx, tblastn, and tblastx have word sizes of

2 or 3. Neighborhood words are never used

for blastn.

Nucleotide scoring Choice of match/mismatch or scoring matrix. Only match/mismatch scoring.

Nucleotide statistics Karlin-Altschul parameters are available for

several match/mismatch values and gap

costs.

Karlin-Altschul ...