[BiO BB] Re: [Bioclusters] [BLAST-Announce #053] BLAST 2.2.13 released]

Martin Gollery marty.gollery at gmail.com
Sun Dec 18 15:04:00 EST 2005


Wow- that is a significant speedup!

I don't mind the minor score differences either- does anyone else?

Marty

On 12/16/05, Mike Muratet <muratem at eng.uah.edu> wrote:
>
> 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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>



--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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