Screening data bases with degenerate DNA sequences?

R. Scott Jokerst scott_jokerst at data-transport.com
Tue Jan 21 16:55:20 EST 1997


Sure!

For example, one might typically do a tblastn BLAST search of one of the
GENBANK databases by querying a nucleotide db with a protein sequence.  All
six reading frames of the nucleotide db are searched for the peptide
sequence of interest.

You can try out this type of searching on the web either at:

        http://www.ncbi.nlm.nih.gov/BLAST/
using:
        http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-blast?Jform=0

or with Baylor's Search Launcher:

        http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html
using:
        http://dot.imgen.bcm.tmc.edu:9331/seq-search/protein-search.html


Hope this was helpful,

Scott

Biological Data Transport
http://www.data-transport.com
****************

At 5:03 PM 1/20/97, Stephan Geley wrote:
>Is there any possibility to screen sequence data bases with degenerate
>DNA sequences derived from short peptide sequences?
>Thanks for your help,
>Stephan

    R. Scott Jokerst (510-648-8229)    scott_jokerst at data-transport.com
       Biological Data Transport       http://www.data-transport.com
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