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

Dinanath Sulakhe sulakhe at mcs.anl.gov
Wed Dec 21 01:07:51 EST 2005

Hi Mike,
I tried running 2.2.13 with -V F option, and one thing i noticed is it 
keeps all the results in the memory and writes to the file only at the end?
Has anyone noticed this. If its true, then its difficult to use this option 
-V F on large input files (thousands of sequences) against a huge database.

I ran a blastall for 1000 protein sequences against non-redundant database 
(ncbi's) using -p blastp and -V F. But i see teh output file is empty even 
after about 15 mins. But if i run the same job without -V F option i start 
seeing output. I have formatted the NR database with -v 200 option.

Please let me know if you have seen an similar behavior. And is it possible 
to flush the output to the file so as to reduce the memory usage?


At 03:24 PM 12/16/2005, Mike Muratet wrote:
>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
>           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
>34   0.19
>32   0.75
>32   0.75
>32   0.75
>30   3.0
>30   3.0
>30   3.0
>30   3.0
>>TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp...
>30   3.0
>So, it looks to be significantly faster.
>Bioclusters maillist  -  Bioclusters at bioinformatics.org

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