[BiO BB] Help with standalone Blast

James Fraser james.fraser at mail.mcgill.ca
Wed Aug 11 12:19:26 EDT 2004


Hello,

I have tried to resolve this problem on two copies of standalone blast (one on
linux and one on windows).  I have created a custom db of 65 sequences:

formatdb -i ig.txt -n ig

Then I ran an all against all blast

blastall -p blastp -d ig -i ig.txt -o ig.out

This worked fine.  The problem is that when I change the e value cutoff (using
-e ) i get odd results.  For example:

running

blastall -p blastp -d ig -i ig.txt -o ig.out -e 1.0

yields:

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

12764866                                                              190  
9e-53
129567005                                                              33  
2e-05
146402107                                                              24  
0.014
133620536                                                              23  
0.018
116798795                                                              22  
0.054
19626396                                                               20   0.27
145686327                                                              20   0.27
19630478                                                               19   0.35

and running

blastall -p blastp -d ig -i ig.txt -o ig.out -e 0.1

yields:

Sequences producing significant alignments:                      (bits) Value

12764866                                                              190  
9e-53
133620536                                                              23  
0.018

My question is: Where did the hits for 129567005 and 146402107 go?  The only
thing I changed is the e value and I reiterate that I have tried this on two
different machines running different OS.

Thank you,

James Fraser




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