[Bioclusters] blast 2.2.9 issues with expect value (-e)

bioclusters@bioinformatics.org bioclusters@bioinformatics.org
Fri, 25 Jun 2004 13:49:32 -0500


Hi,

I just updated my blast from 2.2.6 to 2.2.9 and am suddenly getting very
strange results.  Sequences are appearing to have the same expect value
although the matches in the hsp are very different.  I am wondering if any
one has seen a similar issue.  I am also finding that if I set the -e
option to be higher, I can even get matches with just four bases, although
I have a word size of seven.  Something is going very wrong!

Here are the stats on my machine and blast command + example output:

dual xeon 2.8 GHz, 4GB RAM, OS, RH linux: enterprise 3.0, kernel 2.4.21-9

options on the blast command line:  -W 7,  -e 1,  -i input,  -o output , -d
myinternalblastdb, --p blastn

I'm using precompliled 2.2.9 from the NCBI.


From blast:

> 5846704
          Length = 177

 Score = 24.3 bits (12), Expect = 0.16
 Identities = 18/20 (90%)
 Strand = Plus / Minus

Query: 13  ctccagacattgggcgggtt 32
           |||||| ||||| |||||||
Sbjct: 127 ctccaggcattgagcgggtt 108


> 5714596
          Length = 9401

 Score = 24.3 bits (12), Expect = 0.16
 Identities = 8/20 (40%)
 Strand = Plus / Minus


Query: 13  ctccagacattgggcgggtt 32
             | ||| |     |||
Sbjct: 202 tccaagaaaggacccggtcg 183

-Bonnie