[Bioperl-l] your suggestions please

[R. Chase Southard]

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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