[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
More information about the BBB
mailing list