As a new reader of the bionet.software.gcg news group, I am looking for
answers to a problem that has been bothering me for some time. Students
in my department often will perform homology searches (fasta or tfasta) of
the GenEMBL data base and pull up sequences of low, but they claim,
significant similarity. Clearly, if this were a simple sampling of a
population, they would be expected to demonstrate "significance" to a
specified confidence level. With DNA or protein sequences, we seem to
simply nod and wink at the comparison and say "yeah, that looks
homologous".
I would appreciate your responses concerning how this problem has been
treated and some specific references dealing with this question.
Alan Friedman (6566friedman at vms.csd.mu.edu)
Dept. Biology
Marquette University
Milwaukee, WI 53233
