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,

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. 



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

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