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