importing .msf docs

Jeremy John Ahouse ahouse at hydra.rose.brandeis.edu
Tue Jun 22 09:46:56 EST 1993


In article <jasons-220693150108 at hugo.medgen.uu>, jasons at bmc.uu.se (jason e.
stewart) wrote:
> 
> Anyone know a way to import a file generated by GCG Pileup into a Mac (or
> PC) sequence alignment program. After having used GCG to do the aligning my
> friend wants to add legends and things to his alignment for publishing
> purposes. Since he is familiar with the DNAstar MegAlign program he wanted
> to do it their, but it can't import whole alignments, only single sequences
> in EditSeq format. And since DNAstar's EditSeq won't accept a dash '-'
> character all gaps disappear when you try to process the individual
> sequences.
> 
> Any ideas appreciated.
> 
> Jason.

			This problem with importing is an unfortunate feature of datafiles that
aren't TEXT.  I think the only high priced commercial package that is good
about inmporting and exporting is sequencher.  However there are FreeWare
packages that are wonderful.  Make sure to get SeqApp (It's printing may be
enough for you).  It will read the GCG output (MSF) directly.  Available
from the IUBIO archives, it has been announced on this newsgroup recently.

    If you still want to manipulate the files; save as Pyllip Interleaved. 
The resultant seqApp file (and any seqApp file since they are all TEXT) can
be opened with MSWord.  Once in word learn to use the option select
feature.  This allows you to delete and copy text that covers several lines
(without including the whole lines) and is probably the single best feature
of MSWord.

note: You can use BBEdit to get the sequences to be aligned in columns. 
Use the GREP mode for search and replace.

Search for: \([A-Z\-.][A-Z\-.][A-Z\-.][A-Z\-.][A-Z\-.][A-Z\-.]
[A-Z\-.][A-Z\-.][A-Z\-.][A-Z\-.]\)

Replace with: \1<space>

where <space> is really just a single space character and not the string
"<space>"


        :::::::::::::::::::::::::::::::::::::::::::
        Jeremy John Ahouse
        Center for Complex Systems and Biology Dept
        Brandeis University
        Waltham, MA 02254-9110
        (617) 736-4954
        email: ahouse at hydra.rose.brandeis.edu
        Mail from Mac by Eudora 1.3.1 - RIPEM accepted




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