How Long Does Running Psipred Take ~ 600 Sequences In A Fasta File

Question

[arronslacey]

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?

Thanks.

[Khader Shameer]

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.

[Cacau]

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.

Answer 1

[dimitrius.8d]

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.