Hi,
I have 460 amino acid sequences for a specific protein family X. I want to make a HMM model for those sequences. I will use that HMM to search homologs of X / neighbour of X in some bacterial genomes. How can I make a HMM model ? Is there any software available? What is the step to do that?
Thanks in advance.
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saadleeshehreen
The HMMER software (which is well documented) can be used to produce HMMs from alignments.
As for searching DNA with protein HMMs:
The current HMMER manual (2015, version 3.1) states: "Still missing: Translated comparisons. We’d of course love to have the HMM equivalents of BLASTX, TBLASTN, and TBLASTX. They’ll come."
(Of course, you could always translate your genome in all frames , chop it up, and then screen it using protein HMMs. It is a bit ugly, you might run into some frameshift trouble, but maybe it works?)
To give a bit more details, to build a HMM for a set of proteins, the steps are:
- build a multiple sequence alignment with e.g. Clustal
- run hmmbuild (from the HMMER package) with the multiple sequence alignment as input
Thanks. From their manual I came to know, I need to give .sto file as input to get a .hmm file. Does Clustal give .sto file as output? Or I have to use different software to convert my file after clustal?
Cheers
As far as I remember, hmmbuild can read alignments in several formats. Just check the docs.
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