Question: How to generate a multiple HMM file with HMMER?
gravatar for yarmda
22 months ago by
yarmda0 wrote:

I want to generate a file that contains multiple HMMs, one each for given genes. HMMER documentation says this can be done, if created from a file containing more than one multiple sequence alignments. Further in HMMER docs, it says that a multiple MSA file must be in "Stockholm format," as the writers did not know of another format that could allow for a multiple MSA file.

HMMER can produce Stockholm-formatted MSAs, but it creates them from HMMs, not from actual reads. Creating Stockholm-formatted MSAs with HMMER from an HMM that wasn't produced from a Stockholm-formatted MSA also loses out on the important Stockholm-format MSA headers, so this approach did not work.

My goal is to use HMMER to query HMMs for multiple genes simultaneously or iteratively without needing to specify many different file names. I do not believe i can simply concatenate HMM files, either.

Can anyone suggest a way to produce an MSA in Stockholm format from reads or to work around this problem altogether?

msa stockholm hmmer • 1.5k views
ADD COMMENTlink modified 22 months ago by Sej Modha4.1k • written 22 months ago by yarmda0

Yes, you can simply concatenate HMMER profile HMM files.

ADD REPLYlink written 21 months ago by cryptogenomicon150

Simply copy&paste the .hmm files into one text file? Can you please clarify?

ADD REPLYlink written 4 months ago by andzsci0
gravatar for Sej Modha
22 months ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

According to HMM docs:

hmmbuild reads a multiple sequence alignment file alignfile , builds a new profile HMM, and saves the HMM in hmmfile. alignfile may be in ClustalW, GCG MSF, or SELEX alignment format.

ADD COMMENTlink written 22 months ago by Sej Modha4.1k

SELEX approximates the Stockholm format used by pfam

ADD REPLYlink written 22 months ago by yarmda0
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