[Bioperl-l] Perl Regular Expressions sought that match typical bioinformatics applications input data

Jeffrey Chang jeffrey_chang at stanfordalumni.org
Fri Mar 26 16:53:41 EST 2004

The closest to this that I know about is the set of Martel regular 
expressions in the Biopython package.  It has descriptions for many 
bioinformatics formats and can be used for verification, like you 
requested.  However, they are not Perl style regular expression.  You 
can probably convert them in an automated way, but then your small 
software project would be growing into a middling one...


On Mar 26, 2004, at 3:36 PM, M.Shahid wrote:

> Dear All,
> For a small software project, I'm looking for Perl Regular
> Expressions that match file formats and related input used
> for bioinformatics applications, e.g. FASTA, Clustal,
> PROSITE patterns, PAM similarity matrices, etc. Note
> that I do not want to parse such data, just check whether
> the format is correct. Is there any compilation out there ?
> If not, what is the best starting point to collect such Regular
> Expressions ?
> Best Wishes,
> M. Shahid
> _______________________________________________
> 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