[Bioperl-l] Highlighted short sequences

[Dave Messina]

Hi Jessica,


> Does any one know if there is any existing function of bioperl that can
> locate and highlighted short stretch of nt sequences within long genomic sequences ?


I don't think there is an out-of-the-box BioPerl solution for this.

You're presenting a two-step problem: 1) locate the short stretch 2) highlight it.

For the 'locate' part, that usually means a similarity search with BLAST, BLAT, or something along those lines. There are parts of BioPerl to help run those searches and parse their results.

See http://www.bioperl.org/wiki/HOWTO:Beginners for an introduction.

Once you've found the coordinates of the match, then there are lots of ways you could conceivably highlight the matches.

A simply way, requiring no special code, would be to change the case of the letters:

agctagcatgcatgcAGACTGATCATCagctagctac


Or use HTML:

agctagcatgcatgc<b>AGACTGATCATC</b>agctagctac


For some more sophisticated options, take a look at Bio::Graphics:

http://search.cpan.org/perldoc?Bio::Graphics


Dave