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Rosetta membrane blastpgp/psiblast database problem for lips4 generation

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Rosetta membrane blastpgp/psiblast database problem for lips4 generation

I have run Rosetta membrane successful in the past, but it seems that now the blastpgp database necessary to run the script is obsolete.
In the lastest BLAST release, blastpgp has been dropped entirely in favor of psiblast.
I am then blocked and I cannot generate the lips4 file using: <fasta file> <span file> <path to blastpgp> <path to nr database> <path to script>

Is there a way of the connecting the psiblast, or does it need to be modified?

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Tue, 2014-09-16 11:45

There is currently an effort to update and modernize the membrane related code in Rosetta, which would include the run_lips script, so updating is something that's on the list of things to do, although we don't have it completed currently.

Here's a quick outline of the changes which would need to be made:

The key line of code in with respect to blast is line 80, which basically invokes the command

$PSIBLAST -i $seq -d $DB -j 2 -h 0.001 -b5000 -v5000 -o $blastout

To use the more recent version, it looks like that needs to be changed to

$PSIBLAST -query $seq -db $DB -num_iterations 2 -evalue 0.001 -num_alignments 5000 -num_descriptions 5000 -o $blastout

The output format is also almost-but-not-quite the same, so the script needs to be changed. I've attached a patch file which shows the necessary changes. (This can be quickly applied with "patch < alignblast.patch_.txt" - I'd recommend making a backup copy of the old version before you do.)

Note that I haven't benchmarked these changes - There may be some additional setting/parameter changes you would need to make in order to get equivalent performance from the lips predictions for the psiblast versus blastpgp. Caveat experimentor.

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Wed, 2014-09-17 10:06