multiple sequence alignment

Jason Miller millerj at equity.wharton.upenn.edu
Sat Nov 11 21:09:08 EST 1995


Thanks everybody. I asked for help finding a survey of multiple sequence
alignment software. Many people responded by e-mail. Many others asked me
to post results. Here are the responses (anonymous since they were
mailed). 

-- Jason Miller, University of Pennsylvania, millerj at wharton.upenn.edu

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here is a couple of references that could be of interest for you:

Record 1 of 3 - MEDLINE (R) 1994

TI: Comparative analysis of multiple protein-sequence alignment methods.
AU: McClure-MA; Vasi-TK; Fitch-WM
SO: Mol-Biol-Evol. 1994 Jul; 11(4): 571-92

Record 2 of 3 - MEDLINE (R) 1/95-11/95

TI: Comprehensive study on iterative algorithms of multiple sequence alignment.
AU: Hirosawa-M; Totoki-Y; Hoshida-M; Ishikawa-M
SO: Comput-Appl-Biosci. 1995 Feb; 11(1): 13

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You might look up papers by Martin Vingron who looked at various methos
and the effects of different gap penalties. Meth Enz. Vol 183 has a lot of
relevant stuff. Gaston Gonnet put out a paper in Science a few years back
claiming to have the ultimate solution. IMHO different methods work for
different classes of problem, much as one might not like it. 

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Clustal V in unix and DOS environment. It performes multiple alignment.
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Protein Sequence Alignment and Database Scanning (Geoffrey Barton) 
http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html
mirror:
http://merlin.mbcr.bcm.tmc.edu:8001/bcdusa/welcome.html

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You will find informations and links to multiple alignment programs on the
BioComputing Hypertext Coursebook at:
http://info.mcc.ac.uk/hpctec/courses/Biocomputing/vsns/bcd/Curric/welcome.html

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Consider wavelet models.  It may work.  MATHLAB(R) may do the job.
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Discussion Theme: The MSA algorithm
http://www.techfak.uni-bielefeld.de/bcd/Lectures/kececioglu.htm

A Gentle Guide to Multiple Alignment, (Georg Fuellen)
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/mulali.htm

Multiple Sequence Alignments (Fredj Tekaia)
http://www2.pasteur.fr/~tekaia/MAcours/multalign.html

ClustalW tutorial, (Fredj Tekaia)
http://www2.pasteur.fr/~tekaia/MAcours/clustalw.html

ClustalW tutorial, (Andrew T. Lloyd)
http://biotech.bio.tcd.ie/acerhelp/ClustalW-Acerhelp.RTF.txt.html





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