Path: utzoo!utgpu!watserv1!watmath!uunet!bu.edu!mit-eddie!bbn.com!nic!chaos.cs.brandeis.edu!AHOUSE@BINAH.CC.BRANDEIS.EDU
From: ahouse@BINAH.CC.BRANDEIS.EDU
Newsgroups: bionet.molbio.evolution
Subject: Re: Homology/similarity/identity: proper usage.
Message-ID: <00943D30.C06A65E0@BINAH.CC.BRANDEIS.EDU>
Date: 6 Feb 91 16:46:54 GMT
References: <3824@gazette.bcm.tmc.edu>,<OWHITE.91Jan31142027@haywire.nmsu.edu>
Sender: @chaos.cs.brandeis.edu
Reply-To: ahouse@BINAH.CC.BRANDEIS.EDU
Organization: Brandeis University
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In article <OWHITE.91Jan31142027@haywire.nmsu.edu>, owhite@nmsu.edu (smouldering dog) writes:>
>to refer to two sequences being homologous means they are a  _strict_
>(nucleotide for nucleotide) match.  

Homology is often used with the goal of stating an inference about relatedness. 
You either have sequence identity or if you've looked at it amino acid
identity.  You may wish to indicate that some bases or amino acids are switched
but have the same function...  So all this means that you should be very
explicit about what you intend.  Your reading of homology as "strict" match
replaces a statement about inferred relationship with one about pattern and
seems too restrictive.

Jeremy