[Bioperl-l] Check sequence format, question

Chris Fields cjfields at uiuc.edu
Wed Nov 1 23:28:11 EST 2006

On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote:

> Dear bioperl mailing list,
> I trying to get sequence from a file using Bio::SeqIO, before I do  
> anything,
> I want to make sure that the file is in a correct Fasta sequence  
> format. I
> want it to spit out an error message if it is in any other format.
> What is the easiest way to do it?
> Thanks,
> Eugene Bolotin
> Sladek Lab.

There is no formal FASTA definition that is universally accepted  
beyond having the first line start with '>' and an optional  
description, with the sequence in subsequent lines.


Bio::SeqIO isn't currently set up to validate sequence formats  
directly, but you could try preparsing the data using  


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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