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Sequence Checksum Calculation

Don Gilbert gilbertd at bio.indiana.edu
Thu Feb 17 20:15:11 EST 2000



Here is the GCG checksum algorithm:
	public static long GCGchecksum( Bioseq seq, int offset, int seqlen) 
	{
	  int check = 0, count = 0;
	  byte[] ba= seq.toBytes();
	  for (int i = 0; i < seqlen; i++) {
		byte b= ba[i+offset]; 
		if (b>='a' && b<='z') b -= 32;
		count++;
		check += count * b;
		if (count == 57) count = 0;
		}
	  check %= 10000;
	  return check;
	}

See also http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
for a program that does sequence reformatting, including gcg single
and msf formats.
--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu




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