Problem with GDE & readseq MSF format

L. H. Bell lhb at s-ind1.dl.ac.uk
Wed Aug 24 14:47:22 EST 1994


Hi, 

A while back it was noted that there was a problem with readseqs MSF
format when used in GDE - GDE outputs the gaps as '-' and GCG demands
'.'.  Putting sed in between GDE and readseq cures this problem.

I appear to have run into another problem  - if your sequences vary 
in length so that 1 or more sequences will be placed on an extra 
line, then readseq does not ouput the last line for these longer
sequences, and the MSF files are not acceptable to GCG programs.

It does calculate the checksums correctly though as all you have
to do to get these MSF files working is to edit in the missing
residues. 

I've tried to get round this problem with no luck. Does anyone have
a solution?


Thanks for the help,


Lachlan Bell




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