Question: How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
10
gravatar for Alex Richter
8.5 years ago by
Alex Richter210
San Diego
Alex Richter210 wrote:

I'm attempting to generate an rpsblast database from a set of protein cluster alignments. For most of them, I could use blastpgp -B <alignment> to generate the PSSM without problem, but several of the alignments (namely the large ones, or the ones with huge sequences) crash (seg-fault) blastpgp (legacy v2.2.23, if it matters).

However, these alignments can be hmmbuilt into HMMER profiles without complaint. I know there has to be a way to convert the HMMs to psiblast profiles, since does it for CDD with PFAM and TIGRFAM. I'm just hoping it something better than exporting the alignment, then blastpgp -- particularly since that's what's crashing.

Anyone got a script to convert them directly?

hmm • 2.6k views
ADD COMMENTlink written 8.5 years ago by Alex Richter210

Was the script working or were you able to create your own conversion script? If so, please share your findings because I'm looking into the exact same thing right now.

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k
5
gravatar for iw9oel_ad
8.5 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

This post by Yun He from 2005 on the bioinformatics.org Sequence Search mailing list offers a method via hmmconvert and a script. I haven't tried it myself, nor have I tried to check to see if it's correct.

ADD COMMENTlink written 8.5 years ago by iw9oel_ad6.0k

Looks interesting, although it's missing a couple columns in the PSSM, and I'm not entirely sure where the $your_query_sequence is coming from. I'll have to see if I can get it to work. If nothing else, it'll give me a place to start.

ADD REPLYlink written 8.5 years ago by Alex Richter210
0
gravatar for Niek De Klein
8.4 years ago by
Niek De Klein2.4k
Netherlands
Niek De Klein2.4k wrote:

Can someone explain the script of Yun He? I've never used Perl and I don't understand where I have to put what. If I change the

&read_hmmprof("profile_in_HMMER_format.prof", \@hmmprof);

to my own hmm profile it only prints the effective alphabet and nothing else.

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Niek De Klein2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 891 users visited in the last hour