A problem in Database Searching

Francisco M. De La Vega fvega at cinvesmx.bitnet
Wed Jun 24 18:37:00 EST 1992


        Dear Netters,

        I have a problem in database searching that I hope someone out
there could help me. I am interested in locating genes of E. coli that
end with the UGA stop codon and which partially overlaps the AUG start
codon of the following gene. That is, I am looking for a AUGA pattern,
but just those cases that indeed are gene overlapings.

        I used PatternSearch from the GCG Package, but as most can imagine
the background of all AUGA sub-sequences that does not correspond to real
gene overlapings is enormously high. I dont dare to inspect this output
to locate by hand (looking at each GenBank entry) the real overlapings..

        Does someone knows a software that could do this for me?

        Many thanks,

        Francisco M. De La Vega
        Department of Genetics and Molecular Biology
        CINVESTAV-IPN, Mexico City, Mexico.
        E-Mail: FVEGA at CINVESMX.Bitnet



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