July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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WU-BLAST Parameters
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279
R=[integer]
Default: 10 blastn, 2 blastp, blastx, tblastn, tblastx
Sets the cost for the second and remaining gap characters.
See also
Q
restest
Default: Off
blastp and blastx statistical tests are based on the number of residues (letters) in the data-
base. If
Z is set in conjunction with restest, blastn, tblastn, and tblastx will also be based on
the number of letters.
See also
seqtest, Z
S=[integer]
Default: Variable; calculated from E
Sets the final score threshold. Since S and E are interconvertible through the Karlin-Alts-
chul equation, setting
S effectively sets E, and vice versa. When both are set, the more
restrictive one is used.
See also
E
mS2=[integer]
Default: Variable; depends on scoring parameters
Score threshold for individual ungapped alignments. If both S2 and E2 are set, the more
restrictive one is used.
See also
E2, gapS2, gapE2
seqtest
blastn, tblastn, and tblastx statistical tests are based on the number of sequences in the
database. If
Z is set in conjunction with seqtest, blastp and blastx will also be based on the
number of sequences.
See also
restest, Z
span, span1, span2
Default: span2
WU-BLAST normally discards HSPs that are contained completely within a larger, higher-
scoring HSP. This behavior is called
span2.Ifspan1 is set, alignments are thrown out ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.