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Homology/similarity/identity: proper usage.

smouldering dog owhite at nmsu.edu
Thu Jan 31 16:20:27 EST 1991

In article <3824 at gazette.bcm.tmc.edu> steffen at mbir.bcm.tmc.edu (David Steffen) writes:
>     I am again struggling with the proper use of the words "homology",
>   "similarity", and "identity" in comparing sequences.  Specifically, we
>   have cloned and sequenced (a bit of) the rat homologue of the _lck_
>   etc......
this is a topic worth discussing.  my understanding is that when you
are referring to a sequence that has _some_ nucleotides in a close
approximation to another sequence you should say:
	sequence A has __% similarity to sequence B.  

alternatively you can say:
	sequence A has __% identity to sequence B.

to refer to two sequences being homologous means they are a  _strict_
(nucleotide for nucleotide) match.  as in:

	the cDNA sequence to gene A is homologous to region X of the
genomic clone of gene A.

alternatively you can say:
	the cDNA sequence to gene A is identical to region X of the
genomic clone of gene A.

however, I am curious if the rest of the community agrees with the
above usages of identity, similarity and homology.

owen white

	owen white		(owhite at nmsu.edu)

               got my head on a pole (for better reception)

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