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From: frank@sass.sari.ac.uk (Frank Wright)
Newsgroups: bionet.software
Subject: Re: more on knowing computers
Message-ID: <8176.9104051141@sass.sari.ac.uk>
Date: 5 Apr 91 11:41:44 GMT
Sender: daemon@genbank.bio.net
Lines: 35

I agree entirely with Michael Gribskov's comment.....

"My perception is that, currently, broad conclusions about the function,
 evolution and structure of macromolecules are being made based on
 sequence similarity and inferred homology.  Few graduate programs
 provide the training to critically evaluate such claims, and many people
 are left to either take the claim on faith or to reject it as
 unimportant."

I'm writing a short "introduction to sequence analysis" course
for Molecular Biologists at Scottish Agricultural Research
Interests and am keen to stress that sequence *analysis* is
really what they are doing, and that *computing* is simply the
means to this end.  I feel this is necessary given the use of
"BioComputing" and/or "Molecular Biology Computing" to describe
the activity of sequence analysis as well as the technology that
makes it all possible.

Sequence analysis often involves formulating a model, and analysing
the data assuming that the model is valid.  For example, database
searching programs are implementations of algorithms that make
assumptions about evolutionary processes.  Tradeoffs between
biological reality and mathematical tractability or CPU time are
necessary.  Users should be aware of these when interpreting output.
Some knowledge of subjects like protein structure and evolution are
required when carrying out and interpreting such complex analyses.
..and possibly also statistics... but I realise it's not a word that
one uses nowadays.  I avoid it by using "predict", "sequence analysis",
"structure analysis",etc...   It stops people's eyes glazing over.
                                                                  :-)

Frank Wright
SASS Molecular Biology Support
Edinburgh University, Scotland
e-mail:  frank@sass.sari.ac.uk