Help wanted on alignments

Kevin Karplus karplus at cse.ucsc.edu
Fri Sep 17 11:50:26 EST 1999


In article <Fergus.Doherty-ya02408000R0809991149070001 at news.nottingham.ac.uk>, Fergus.Doherty at nottingham.ac.uk (Fergus Doherty) writes:
|> Problem:  I want to align a domain present in a superfamily of proteins
|> against a specific example of that domain. Er..that is to generate a large
|> number of pairwise alignments of the different examples of this domain
|> against my target sequence  (at leat I think that is what I want to do?),
|> and then order them in respect to similarity/identity. Is there a program
|> that will do this in a single pass?


The task sounds like an ideal one for the SAM package, which is
available free to universities.  See http://www.cse.ucsc.edu/research/compbio

Build a model from an alignment consisting of just your domain
sequence (even better, from a multiple alignment of domain sequences)
using "modelfromalign".

Use "hmmscore" to score all sequences in your superfamily.   You can get
alignments and scores from hmmscore in one pass.

If you want to refine the domain definition, you can use "buildmodel"
with the initial model from your single sequence and the unaligned
superfamily sequences.  This produces better alignments, but the
scores become rather meaningless (all the sequences are in the
training set, so they all score well).

The next release of SAM (coming soon) will include some scripts to
make tasks like this a single command, and we'll put up some web pages
that call the scripts, but the particular task you describe is easy
enough with the current release.  Contact us if you need help.

-- 
Kevin Karplus 	karplus at cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck

-- 
Kevin Karplus 	karplus at cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck





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