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

Joe Landman bioclusters@bioinformatics.org
Fri, 25 Jun 2004 14:57:27 -0400


Hi Bonnie:

  Could you share the sequence and one of the lines in the DB that matches?

Joe

BHurwitz@twt.com wrote:

>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
>
>
>
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>  
>


-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
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