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Subject: CSLG|COMMENTARY: From Andrew Coulson
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Date: Fri, 4-Dec-87 22:16:40 EST
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Posted: Fri Dec  4 22:16:40 1987
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From: Sunil Maulik 

 4-Dec-87 12:33:43-PST,9076;000000000001
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       Searching large databases for sequence similarities.

         Ellis Golub asks whether good searching methods find anything of
biological interest. You bet they do! Our best case so far is still in press
with PNAS (Bownes, M., Shirras,A., Blair,M., Collins,J. and Coulson,A.
"Yolk protein degradation times release of ecdysteroid in insect
embryogenesis."), but two that have already appeared are in Nature 1987,326,
614-617 and 328,766.
         We have not applied this method very much so far to DNA databases; the
main reaon for this is lack of resources (= personnel), but there are also
scientific reasons.
For any cistron, it is always better to perform searches and comparisons at
the protein level (see Collins J.F. and Coulson,A.F.W. "Molecular sequence
comparison and alignment" in  Bishop,M.J. and Rawlings,C.J. "Nucleic Acid
and Protein Sequence Analysis a Practical Approach", IRL, Oxford, 1987, pp
323-358, if you need convincing); and in any case there is really no scope
for sophisticated matching scores in nucleic acid comparisons.
Nor do we have much general information about the accepatibility
of gaps in non-coding nucleic acid sequences.  My feeling
is that pattern detection methods are really what is appropriate for
nucleic acid database searching, rather than the NWS algorithms.
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