checksum?

[Peter Stockwell]

David Saul (dj.saul at auckland.ac.nz) wrote:
> Can't find this in the documentation.
> Can anbody tell me how the checksum is calculated in GCG formated sequences.
> Also each sequence in an .msf file has its own checksum but there is
> another in the header. What is this calculated from?

The information is given in the documentation, though it can take time to
find.

There are two different algorithms, 1 for general text and the other for
sequence data.

A Pascal implementation of the sequence algorithm is:

function upcchr(achr: char): char;
  begin
  if (achr in ['a'..'z']) then
    upcchr := chr(ord(achr) + ord('A') - ord('a'))
  else
    upcchr := achr;
  end;

function uwcheckinc(sptr: integer;
                    residue: char): integer;
{ returns the incremental value for this position and base in UW 
  checksum }

  begin
  uwcheckinc := (1 + ((sptr-1) mod 57))*ord(upcchr(residue));
  end;  { of uwcheckinc }

function uw_sumcheck(var seq: packed array
                       [lb..ub: integer] of char;
                     slength: integer): integer;
{ returns accumulated total checksum for UWGCG based on contents
  of array, and length.  Case-independent. }
  var
    sptr: integer;
    sum: integer;

  begin
  sum := 0;
  for sptr := 1 to slength do
    sum := sum + uwcheckinc(sptr,seq[sptr]);
  uw_sumcheck := sum;
  end;      { of function uw_sumcheck }

============================================================

Peter A. Stockwell
Dept of Biochemistry,
University of Otago
Dunedin, New Zealand.

> Thanks in advance

> Dave Saul
> -- 
> David Saul                          dj.saul at auckland.ac.nz
> School of Biological Sciences       Tel 64 9 3737599 Ext 7712
> University of Auckland              FAX 64 9 3737414
> Auckland Private bag 90219
> New Zealand