Modifying an MSF file ?

Mike Mitchell mike at bison.lif.icnet.uk
Tue Jun 6 04:35:52 EST 1995

In article <3qoqh2$nve at senator-bedfellow.MIT.EDU>, lluis at aaRS (Lluis
Ribas) wrote:

>    Hi, 
>    I am having troubles modiifying a PileUP MSF file
>    by hand for which I wnat, later, to obtain a 
>    profile with PROFILEMAKE.
>    Basicly I am taking the MSF file, editing it manually,
>    and trying to use it with PROFILEMAKE. But the program
>    claims that the alignment is not in GCG format.
>    I have copied scrupously the format of the original
>    MSF, modified the sequence lengths according to the new
>    alignment and checked the document format very
>    carefully, but to no avail.
>    The only thing I cannot change are the Check values
>    which I just leave unaltered.
>    Any idea of what is happening and whether there is a
>    solution ?

Are you using a text editor to edit the alignment? If so this is almost
certainly why ProfileMake is not happy with your sequence. You will need
to use Reformat to get the file sorted out. Alternatively you might try
using LineUp, which is a GCG aligment editor that formats the msf properly.

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