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[Q]: GCG sequence checksum calculation

Conrad Halling chhall at bb1t.monsanto.com
Mon May 23 18:15:52 EST 1994


In article <1994May18.120243.206808 at uctvax.uct.ac.za>,
      bbbbre01 at uctvax.uct.ac.za (Brendan Babb) wrote:

> I have written a simple program to convert sequence format.  Howver, I need to
> calculate the correct Check for GCG format files.  Could someone please email
> me at bbabb at medmicro.uct.ac.za with information regarding how the sequence
> checksum is calculated.

On page 28 of the Procedure Library Manual, the function that calculates
the checksum is given:

CheckSeq =
  Mod(Sum of (1 + Mod(Pos-1,57) ) * IChar( CHTOUPPER(Strand(Pos)))),10000)
    for (Pos = 1, length)

IChar( CHTOUPPER( Strand( Pos ))) returns the integer value of the
uppercase nucleotide symbol (A,C,G,T,...) on the positive (upper) strand. 
For ASCII characters, A = 65, C = 67, G = 71, etc.
-- 
Conrad Halling
Computational Molecular Biologist
Monsanto Co., St. Louis



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