[BiO BB] sequence analysis

Mike Marchywka marchywka at hotmail.com
Tue Oct 23 21:13:28 EDT 2007

> > > >   I am interested to find tetramer peptide matching 100% to the
> > > > carboxyl terminal of the protein sequences from human. Is there any
> > > > specific tool available to do so.
> > > >   Can BLAST or FASTA handle it by changing the parameters.

I took a quick look at BLAST documentation and didn't find anything.
I also tried standard PERL regex anchors $ and ^ but didn't seem to work.

What is your objective? I've had a heck of a time with downloaded prosite 
rules that have
anchors as I have to turn them off for translation products from non-edited
transcripts. The reason I mention this is that you may in fact not want to 
yourself until you see what the other hits look like. With only a few acids
you may have to sort through a lot of hits but also see if the conserved 
tools offer any help as apparently some of these can be position sensitive.

I've got my own code that does the opposite of what you want ( :) ).
That is, given a few hundred sequences and some patterns in the form of
PERL regex, I can find each one in each sequence and use this information 
alignment and clustering ( at least that is the hope, and initial results 
don't look

If there is a real need , I guess I could modify this to do the opposite.
That is, if you get a few 1000 proteins that contain your query anywhere,
and  you can't separate with existing
tools but you can phrase your query as a PERL regex, I may have something 
that helps.

But, sure you can just download all the blast hits that have your peptide 
and grep for all the occurences ( this can be a hassle as some straddle line 
etc) anchored to the end.

Mike Marchywka
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