Question: Realignment Of A Protein Domain After Global Multiple Sequence Alignment
gravatar for miquelduranfrigola
6.5 years ago by
miquelduranfrigola760 wrote:

Hi all,

my protein of interest has a length of aka 300 residues. I do a global multiple sequence alignment with a set of homologs and I obtain a phylogenetic tree from there. So far so good.

Now, for a subsequent task, I need to have an accurate MSA of a region of interest of about 50 aminoacids, and I do not care much about the rest. So, what would you guys do in this case? Do I build (or fetch from Pfam) an HMM profile of this region and align with hmmalign? Do I perform a local alignment? How, and with what input?

Thanks a lot!

ADD COMMENTlink written 6.5 years ago by miquelduranfrigola760
gravatar for Rm
6.5 years ago by
Danville, PA
Rm7.8k wrote:

Yes, you can follow Hmm as one of the approaches. I remember very long time back (2003 or so) I used Jalview to address similar problem.

ADD COMMENTlink written 6.5 years ago by Rm7.8k

Definitely. Grab the HMM from PFAM and then use HMMER3 to realign the domain

ADD REPLYlink written 6.5 years ago by Dan Gaston7.1k

Would jackhmmer do as well? I enter my region of interest as input, and all sequences of interest as database, and then iteratively align the region of interest using the hmm profiles. With this, I would skip using predefined PFam domains (which I want in some cases).


ADD REPLYlink written 6.5 years ago by miquelduranfrigola760

You could, I've never done it that way so I'm not sure how well it would work. Are there cases where you don't have a PFAM profile for your region of interest/domain? I have had some success doing iterative hmmer alignments. Start with say MAFFT to generate the initial alignment, which will usually get the domain approximately correct anyway, chop, generate a profile, and realign. Generate a new profile, realign, etc. Do it a few times until it seems to converge.

ADD REPLYlink written 6.5 years ago by Dan Gaston7.1k
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