[Bioperl-l] domain aligned global protein multiple sequence alignment

[Jason Stajich]

We use DIALIGN for this type of problem of multi-copy domain proteins. http://bibiserv.techfak.uni-bielefeld.de/dialign/

or you can use bioperl to parse a HMMer report, get the domain locations, cut all these out and make a multiple alignment of the domains alone if you want to see the history of them.  For our project on such a family we present the domain tree/alignment and also the whole protein sequence history.

jason
On May 6, 2011, at 12:30 AM, onlyIDleft wrote:

> 
> Are there tools in BioPerl that will allow me to obtain multiple sequence
> alignment of proteins but with a twist
> 
> All the proteins I deal with have at least one protein domain (as defined by
> Pfam HMM models)
> 
> So I want to constrain this global multiple sequence alignment with the fact
> that all domains should be aligned to one another....
> 
> I could do it iteratively by using HMM align in HMMER3 for each domain, and
> then use this alignment as a constraint for the global alignment by T-COFFEE
> or some such strategy.
> 
> But this is too manually intensive and cumbersome, are there BioPerl tricks
> that can be used to achieve my goal?
> -- 
> View this message in context: http://old.nabble.com/domain-aligned-global-protein-multiple-sequence-alignment-tp31556697p31556697.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
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