[Bioperl-l] Count amino acid frequency

Brian Osborne brian_osborne at cognia.com
Fri Jun 27 12:52:51 EDT 2003


Stephan,

Are all of your protein variants guaranteed to be of the same length?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Stephan Bour
Sent: Friday, June 27, 2003 11:35 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Count amino acid frequency

I¹m new to the list and bioperl so I hope this is not too stupid a question.

I need to write a perl script that does the following:
- Take a file with about 1000 sequences of the same protein in FASTA format
- For each position on all sequences count the number of occurrence of each
possible residue
- Return only the count of the residues actually present at each position
(in other words, residues present 0 times are not returned).
- Present the data in tab delimited format that could be imported into Excel
for graphing

It is a fairly simple script to write but I try to apply the
do-not-reinvent-the-wheel dogma.

Is there a bioperl module or an existing script that would fit the bill?

Thanks,
Stephan.


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