Question: How Long Does Running Psipred Take ~ 600 Sequences In A Fasta File
gravatar for arronslacey
6.8 years ago by
United Kingdom
arronslacey260 wrote:

Hi - I have been running psipred on a fasta file containing around 600 sequences form the transport protein database. it's been running for about 2 days now.........if the program has stopped then there is no output indicating that this is so. does anybody have any experience with this? how long has it taken you to run fasta files of this size through psipred?


fasta • 2.0k views
ADD COMMENTlink modified 5.3 years ago by dimitrius.8d0 • written 6.8 years ago by arronslacey260

This depends on the mode you are using to run PSIPRED. If it is homology-search enabled version, length of the search will depends on your PSI-BLAST settings.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Khader Shameer18k

Yes. I agree with Khader. Also, the database that you were blasting against can also have an impact on the speed. I think in the manual there is a suggestion of minimizing the database using a simple tool.

ADD REPLYlink written 6.6 years ago by Cacau470
gravatar for dimitrius.8d
5.3 years ago by
United States
dimitrius.8d0 wrote:

It is an old topic, but running with the default options for psiblast and uniref90 as db, each sequence takes about 15 minutes in 16 cores of Xeon-E5 processors.

ADD COMMENTlink written 5.3 years ago by dimitrius.8d0
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