Eric L. Cabot (elmo at helix.nih.gov) wrote:
: Hello world!
: Can someone please supply me with the exact specification
: of the GCG-MSF format. I need it for a program that I am writing.
: More specifically, I would like to have my program produce multiple
: sequence files that can be used by the appropriate GCG programs.
: I sent a similar email query to help at gcg.com a couple of weeks
: ago but go no reply!
:: It sure would be nice if there was a utilitity that took one of
: the cleaner formats, oh-say Fasta or PIR/NBRF, and converted to
: MSF -- but there isn't.
You could convert from a PIR multiple sequence file to a GCG
MSF file in a two step procedure:
1. Convert from PIR to plain GCG sequence format using FROMPIR:
$ frompir myseqs.pir
will create a bunch of files named seqname.gcg extracted from
your PIR file in your current directory.
2. Reformat these GCG sequences into on a MSF file:
$ reformat /msf
[... some info on REFORMAT]
REFORMAT what sequence file(s)? *.gcg
^^^^^
Enter answer here
After specifying the MSF's filename, REFORMAT creates a MSF file
containing the sequences from the original PIR file (if you didn't
have any previously existing *.gcg file in the working directory).
Writing your own stuff to create GCG formatted sequences is
always messy -- at least, I know someone who once tried and
failed to find any documentation on the checksum algorithm,
so he finally figured it out by guessing.
Greetinx, Jan
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