[BiO BB] A series of Pairwise alignments

Martin Gollery marty.gollery at gmail.com
Sun Jun 4 11:57:26 EDT 2006

Hi Mike,

Yes, I have used the PRINTS tools- they are a very useful part of Interpro,
and can be used with InterProScan or stand-alone.


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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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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