[Bioperl-l] Highlighted short sequences

[Chris Fields]

On Jun 4, 2010, at 5:47 PM, Dave Messina wrote:

> 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

GBrowse (via Bio::Graphics) does highlighting for text searches, so you could probably dig out the code used for that as a start.

chris