Andrew Martin amartin at stagleys.demon.co.uk
Fri Jul 24 15:12:54 EST 1998

Chris Sinclair (sinclair at biochem.purdue.edu) wrote:
: O.K. this is a really simple one. I need to calculate the % identity of
: some peptides (10 to 19 residues) to a much longer sequence (499 aa). If
: the peptide is 10 aa long and has 3 exact matches do I divide by 10 (the
: length of potential identity for peptide) or divide by the total length
: of the protein. I personally vote for the first calculation but I've met
: resistance from my fellow lab mates. Anyone care to clear up our debate?

: Thanks,

: Chris

: sinclair at biochem.purdue.edu

Depends why you are doing it and what you are trying to show...
My nw sequence alignment program gives every percentage you could
think of. My personal preference for most normal tasks is to
calculate the percentage over the alignment length. For two
near-similar length sequences this then accounts for the insertion
of gaps as a kind of penalty. But you can also do that without
the tails, or if you are modelling, you are more likely to
want to know the percentage of residues from the target sequence
are found in the parent you are using to model.

In your case of a short peptide against a long sequence it is
pretty meaningless to calculate the percentage over the long

Andrew Martin,

BSM Unit,
Biochem Dept.
University College London

(reading news from home....)

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