[Bioperl-l] your suggestions please

[Jason Stajich]

I'd just use fuzznuc from EMBOSS. depends on whether you only care  
about exact matches and whether or not you want gaps.

On Nov 11, 2005, at 10:07 AM, R. Chase Southard wrote:

> I'm interested in finding a specific nuclear receptor response  
> element (PPRE, ~13 bases, consensus TGACCTnTGACCT)  in either  
> genomic or selected gene promoter regions. After some searching,  
> I'm unsure which method/tool I should use to match this cis-element  
> sequence to unknowns.
>
> Would any of the following be more appropriate than another?
>
> 1. Simple Perl Regex
> 2. Hidden Markov Model
> 3. Bio::Tools::SeqPattern
> 4. Blast2seq - although, I thought that 13 bases may not be enough  
> for blast
> 5. An application in EMBOSS or EMBASSY
>
> Thanks,
>
> Chase
>
> R. Chase Southard
> Research Analyst
> Molecular and Biomedical Pharmacology
> UK College of Medicine
> 800 Rose St MS305 UKMC
> Lexington, KY 40536
> 859-323-2604(p)
> 859-323-1981(f)
> Chase.Southard at uky.edu
> http://www.uky.edu/~rcsout0/
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12