Question: Hmmer for protein prediction
0
gravatar for vishalchanda364
10 months ago by
vishalchanda36420 wrote:

Hello, Regarding using the Hmmer (3.1b1) my requirement is to search amino acid sequences of predicted protein products against an HMM database prokaryotic viral orthologous groups. Which I know can be done using hmmscan.

The user guide says hmmpress has to be performed to prepare a database to run hmmscan on the the test file. But the vog file from the website ( http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads.html ) downloads a tar.gz file and hmmpress asks for a Hmmer3 file. I have no idea about this step and getting confused over it.

Can anyone help me in this reagrds,Please?

next-gen assembly genome • 307 views
ADD COMMENTlink modified 10 months ago by Mensur Dlakic7.2k • written 10 months ago by vishalchanda36420
1

you will for sure have to unpack the tar.gz file you downloaded (it will normally contain a number of other files)

tar -zxvf <download.tar.gz>

should do the trick

ADD REPLYlink modified 10 months ago • written 10 months ago by lieven.sterck9.0k

Yes, I had already done that. Thank you.!

ADD REPLYlink written 10 months ago by vishalchanda36420
1

ok, so what was in the un-zipped tar file then? I'm guessing nothing that could be used for resolving your issue?

ADD REPLYlink written 10 months ago by lieven.sterck9.0k

Thank you for the help.

ADD REPLYlink written 10 months ago by vishalchanda36420
3
gravatar for Mensur Dlakic
10 months ago by
Mensur Dlakic7.2k
USA
Mensur Dlakic7.2k wrote:

hmmscan scores a database of HMMs vs. a database of sequences. An HMM database is what needs to be processed by hmmpress.

Download:

wget http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/Ampullaviridae/AmpullaviridaevogHMMprofiles.tar.gz

Unpack:

tar -zxvof AmpullaviridaevogHMMprofiles.tar.gz

Concatenate HMMs into a database:

cat AmpullaviridaevogHMMprofiles/*.hmm > Ampullaviridae_all.hmm

Press:

hmmpress Ampullaviridae_all.hmm

Scan:

hmmscan Ampullaviridae_all.hmm your_sequences.fasta > search_output.txt

You may want to delete a directory with individual HMMs:

rm -rf AmpullaviridaevogHMMprofiles
ADD COMMENTlink written 10 months ago by Mensur Dlakic7.2k

Thank you so much sir. You're a gem, I was struggling with this since 3 days.

Thank you so much

ADD REPLYlink written 10 months ago by vishalchanda36420
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