July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Further Reading
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but a warning is issued that informs you that you can provide your own values for
lambda, k, and H on the command line.
NCBI’s version of BLASTN doesn’t contain gapped values for lambda; lambda is
always calculated directly from the match/mismatch scores. Because of this, equiva-
lent alignments may have much higher bit scores (and lower E-values) in NCBI-
BLAST than WU-BLAST, even if their match/mismatch scores are identical.
Further Reading
The following papers describe BLAST algorithms in more detail:
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J.
Lipman (1990). “Basic local alignment search tool,” Journal of Molecular Biol-
ogy, 215:403-10.
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang,
Zheng Zhang, Webb Miller, and David J. Lipman (1997), “Gapped BLAST and
PSI-BLAST: a new generation of protein database search programs,” Nucleic
Acids Research, 25:3389-3402.
Gish, Warren and David J. States (1993). “Identification of protein coding regions by
database similarity search,” Nature Genet., 3:266-72.
For the latest information on NCBI-BLAST and other helpful documents, see the
official web site at http://ncbi.nlm.nih.gov/BLAST.
The WU-BLAST web site (http://blast.wustl.edu) has several useful documents on
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