Malay curiouser at ccmb.ap.nic.in
Sun Jul 26 10:40:13 EST 1998

>On 23 Jul 1998 21:44:41 GMT, tpwalsh at acer.gen.tcd.ie (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:
>>DEFGAKSDEHTPQTKVFTS    Alignment is 10 residues long Seqn ID=3/10=30%
>>    *  *    *
>>    ARCD--KVSGQSRL     Alignment is 12 residues long Seqn ID=3/12=25%
>>    *  *      *
>>    ARCDKVSGQSRL       Alignment is 10 residues long Seqn ID=3/10=30%
>>    *  *    * 
>The length that sequences are aligned over isn't always obvious in a
>global alignment, is it?  Sometimes you may want to consider stretches
>of residues at the ends, sometimes you don't.  I think the choice of
>which peptide length to divide by depends on your protein of interest:
>If you're looking to compare the relative homologies of a set of
>proteins to protein A, divide by protein A's length.  
>Al Wang
>remove NOSPAM to reply
In a gapped alignment count also the length of the gap 

Malay Kumar Basu
Centre for Cellular and Molecular Biology
Hyderabad 500007

Fax: (00-91)40-7171195
Phone: (00-91)40-7172241
Vote anarchist.
curiouser at ccmb.ap.nic.in

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