% IDENTITY QUESTION

[Tom Walsh]

In article <35B7B542.2A3D5E5B at biochem.purdue.edu>,
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?

 You divide by the length that the sequences are aligned over:


    ARCDFRSGQSRL
DEFGAKSDEHTPQTKVFTS    Alignment is 10 residues long Seqn ID=3/10=30%
    *  *    *

    ARCD--KVSGQSRL     Alignment is 12 residues long Seqn ID=3/12=25%
DEFGAKSDGQRMTRQWKVMK
    *  *      *

    ARCDKVSGQSRL       Alignment is 10 residues long Seqn ID=3/10=30%
DFGAAKSD---AQTKSHTRE
    *  *    * 

-- 

The Borderite's Prayer ( as revealed to the Prophet Unki):

Thank God the border is there to save us from the mad sectarian bastards.