[BiO BB] A series of Pairwise alignments

Shameer Khadar skhadar at gmail.com
Sat Jun 3 10:51:24 EDT 2006

* Please try FMALIGN @ NCBS
* <http://www.ncbs.res.in/%7Efaculty/mini/FMALIGN/home.html>

This server aligns two or more sequences by fixing sequentially conserved
region or motifs within the aligned sequences. By fixing conserved regions
this method allows flexibility and accuracy to the alignment. It also
provides conserved regions for a set of sequences which can be used for

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Shameer Khadar

Prof. R. Sowdhamini's Lab


On 6/3/06, Mike Marchywka <mmarchywka at eyewonder.com> wrote:
> Yeah, it occured to me the objective would drive the definitions.
> I've been thinking about stuff like this from the immune's system point of
> view.
> Consider something like clustering software since with that many
> sequences they probably can be lumped into clusters. It occured to me you
> could
> take each sequence, break it up (generate "words" (peptides) using your
> favorite epitope
> prediction code ), and cluster the sequences based on "vocabulary".
> This may tell you which groups of proteins look similar to the immune
> system.
> btw, has anyone used tools or features like the "signatures" mentioned
> here?
> http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/printscontents.html#Receptors
> *************************************************************************
> -----Original Message-----
> From:
> bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org
> [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati
> cs.org]On Behalf Of Ann Loraine
> Sent: SaturdayJune-03-2006 10:00 AM
> To: The general forum at Bioinformatics.Org
> Subject: Re: [BiO BB] A series of Pairwise alignments
> Howdy,
> Probably you would want to run a pairwise alignment program over each
> pair of seqs and then write some wrapper code around that to process
> the data as you like.
> The alignment program you select should be something that fits your
> goal - do you want global or local alignment? What kind of scoring
> system do you need? And so on.
> For fun, take a look at:
> http://helix.biology.mcmaster.ca/721/outline2/node42.html
> -Ann
> \
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