Hmmer for protein prediction
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18 months ago

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?

Assembly genome next-gen • 544 views
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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

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

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Thank you for the help.

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18 months ago
Mensur Dlakic ★ 12k

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

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

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

Thank you so much