[Bioclusters] [BLAST-Announce #053] BLAST 2.2.13 released]

Mike Muratet muratem at eng.uah.edu
Fri Dec 16 16:24:32 EST 2005


Greetings

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 
SSGI.021105.

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

yielding

           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] 
139   4e-33
< AJ656543 
34   0.18
< BP160342 
32   0.73
< TC237977 
32   0.73
< TC212301 
32   0.73
< CJ009554 
30   2.9
< AJ657806 
30   2.9
< BI344938 
30   2.9
< AJ651764 
30   2.9
< TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp... 
30   2.9
---
> NP1115201 GB|AY277629.1|AAQ24490.1 type XVII collagen [Sus scrofa] 
138   6e-33
> AJ656543 
34   0.19
> BP160342 
32   0.75
> TC237977 
32   0.75
> TC212301 
32   0.75
> CJ009554 
30   3.0
> AJ657806 
30   3.0
> BI344938 
30   3.0
> AJ651764 
30   3.0
> TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp... 
30   3.0

So, it looks to be significantly faster.

Cheers

Mike


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