Conversion of MSF to Fasta frmat

Michael Coyne mjcoyne at warren.med.harvard.edu
Mon Dec 4 16:21:35 EST 1995

In article <49jrme$19e at mark.ucdavis.edu>, ez041797 at dale.ucdavis.edu
(Jean-Manuel Henry) wrote:

> Hi ,
>       I am trying to use the program MACAW to identify heterologous
> regions in a set of sequences. The problem is that the program seems to
> only accept Fasta format , does anyone know how to convert gcg msf files
> to fasta format ?
> Thanks


MACAW does it's own alignment, and therefore wouldn't need the MSF file
created by GCG (assuming thje MSF file is an alignment, like output from
PILEUP).  If this is the case, and you have the files you fed into PILEUP,
just use the GCG program TOFASTA to put the files in fasta format.  The
TOFASTA program accepts wildcards in the input filename, thus *.pep would
load all matching files into a single fasta format file (which is what
MACAW needs).

Am I missing something here?

Hope this helps...

Mike Coyne

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