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Sequence Checksum Calculation

Paul Roy proy at rsvs.ulaval.ca
Thu Feb 17 18:13:21 EST 2000


Dear "gc"
     I believe you can use Reformat.  The GCG manual says:

                If you edit hsp70.msf with a text editor to manually
                adjust the alignment, you must use Reformat to rewrite
                the MSF file so that it can be used with Wisconsin
                Package programs by using


                      % reformat -MSF hsp70.msf{*}

An MSF file with an incorrect checksum (but otherwise correct) would be
the same as one which has been changed with a text editor.  Reformat would
assume the sequence characters are meant to be correct and calculate a new
checksum.

******************************************************************************

 Paul H. Roy                             Phone:  +1 418 654 2705
 Departement de biochimie,FSG            FAX:    +1 418 654 2715
 Universite Laval                        E-mail: proy at rsvs.ulaval.ca
 Quebec, QC  G1K 7P4
 CANADA

******************************************************************************
     

On Thu, 17 Feb 2000, gc wrote:

> Does anyone know the algorithm that's used for the sequence
> checksum calculation by GCG programs.
> 
> I have .msf output from a non-gcg program which I want to
> use as input for gcg.  Unfortunately, gcg refuses to
> read the sequences, and I think it is because of an incorrect
> checksum value.  If I can get the algorithm I can fix the
> checksums in my .msf files manually.
> 
> Thanks.
> 

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