[BiO BB] Re: [Bioclusters] [BLAST-Announce #053] BLAST 2.2.13 released]
muratem at eng.uah.edu
Fri Dec 16 16:24:32 EST 2005
I ran a test on the the 2.2.13 BLAST that I thought the list might find
interesting. (Thanks to Joe Landman for putting it on the list, I thought
I was on that particular NCBI distribution but never saw the message until
Joe put it here.)
I made a database out of the TIGR gene index for pig, SSGI.021105
I made a test query out of 200 70mers based on 5 sequences from
I ran on a simple test on a Solaris/Sparc64 using
time blastall [-V F] -p blastn -i test.fa -d SSGI.021105 > test.blast
2.2.12 2.2.13 no -V 2.2.13 with -V F
user 1m 39.8s 1m 50.3s 0m 9.2s
real 1m 46.9s 1m 57.7 0m 9.5s
sys 0m 6.3s 0m 6.3s 0m 0.3s
A diff on the output between v.12 and v.13(no V -F) produces only
differences in the header because the version numbers are different.
The diff between v.13(no V -F) and v.13 produces small differences in the
scores and e-values. For example:
< NP1115201 GB|AY277629.1|AAQ24490.1 type XVII collagen [Sus scrofa]
< TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp...
> NP1115201 GB|AY277629.1|AAQ24490.1 type XVII collagen [Sus scrofa]
> TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp...
So, it looks to be significantly faster.
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