Screening data bases with degenerate DNA sequences?

Hiranya Roychowdhury hroychow at NMSU.EDU
Tue Jan 21 11:35:28 EST 1997


At 10:48 PM 1/20/97 GMT, Stephan Geley wrote:
>Is it possible to screen sequence data bases with degenerate DNA 
>sequences obtained from peptide sequencing? Which data base allows the 
>input of ambigous sequences? I would be grateful for any tips,
>Thanks
>Stephan
>
>
>
>

In my experience, short sequences (as you would expect in an oligo eg. 15-60bases) return too many hits to even allow a visual screening. However, I would like to know if there is such an engine in the cyberspace which allows degenerate homology search. Presently, the blast is the only one allowing matches in 6 frames, yet the redundancy in the so called non-redundant libraries (gb, embl, est etc.) makes it rather difficult to sift through hits representing short sequences (100-300bases). I wonder, if it will be better to use blastp for your search first, and then use CLUSTAL or a similar program to look at the returned sequences against your own. 

regards,

HIranya

Dr. Hiranya Sankar Roychowdhury
Plant Genetic Engineering Lab.
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at nmsu.edu



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