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

Fernan Aguero bioclusters@bioinformatics.org
Fri, 25 Jun 2004 16:15:08 -0300


+----[ BHurwitz@twt.com <BHurwitz@twt.com> (25.Jun.2004 15:56):
|
| Sequences are appearing to have the same expect value
| although the matches in the hsp are very different. 

The question you should be asking is why the alignments
below have the same score. If they have the same score,
they'll have the same E value, since the E value is (by
definition) the number of alignments with a score >= S (24.3
bits in this case) that you expect to occur by chance.

Have you indexed the databases using a 2.2.9 formatdb?
Perhaps you're using databases indexed with an older
formatdb?.  I've also seen strange results myself in the
past, and the problem was that somehow the indices created
by older versions of formatdb would not be properly read by
the newer blast executables.

Hope this helps,

Fernan

| 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
|
+----]

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan