[Bioperl-l] Count amino acid frequency

Stephan Bour sbour at niaid.nih.gov
Fri Jun 27 13:29:58 EDT 2003

Good question. There should be an array length test to eliminate any
sequence that's not full length (81 aa) or don't start with a methionine.

> 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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list