CLUSTAL -> MSF convertor

Michael A. Lonetto lonetto at CGL.UCSF.EDU
Fri Mar 29 22:47:32 EST 1996

>Thank you for your comment.
>In article <4jdjbm$mn7 at ratatosk.uio.no> rodrigol at biotek.uio.no (Rodrigo
>Lopez) writes:
>> ClustalW can write GCG's MSF format. Please check the following WWW page:
>I know that. But I have already aligned 8000 bp x 20 seqs.,
>which took me about a week to get the result. So, I would like
>to convert it to MSF.
>I tried to use readseq, but failed:

I may have something that will work.  I wrote a program to convert MACAW
output to pearson format.  I just tried it on a ClustalW "align" format
file, which I believe is the same format as ClustalV output, and it
appears to work.  It will also convert the "-" from clustal into "." for
GCG.  GCG can read the resulting Pearson (Fasta) format file with
"frompearson", then "reformat -msf".

NOTE:  This is an UGLY program, written in portable ansi C with a clunky
command line interface (you have to type in the filename and the number
of sequences).  It does have the benefits of being very small, very fast, and
using very little memory.

If that's OK I can mail you either 1) source code or 2) Macintosh
executable.  I trashed all my other executables and don't have
time spend on this right now.  Let me know if you want it.


Michael A. Lonetto   lonetto at cgl.ucsf.edu
UCSF Dept. of Stomatology, 513 Parnassus Ave, San Francisco, CA 94143-0512

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