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MSF representations for publication

Rodrigo Lopez rodrigol at biomaster.uio.no
Fri May 27 07:46:58 EST 1994


In article <940526081743.20406892 at JAGUAR.CSC.WSU.EDU>, THOMPSON at JAGUAR.CSC.WSU.EDU ("Steve Thompson: VADMS genetics") writes:
|> Hi everybody -
|> 
|> In message <1994May26.121358.5428 at alw.nih.gov> Brian Moldover 
|> (brianm at falcon.dcrt.nih.gov) wrote:
|> 
|> >Here's an interesting question that I had yesterday. We were doing a multiple
|> >sequence alignment for publication using plieup of nucleic acid sequences. 
|> >The person wanted to be able to display the one letter AA symbol above their
|> >novel sequence, with the rest of the alignments below.
|> 
|> >I couldn't think of a way to do this other than cut-and-paste with a word 
|> >processor using the translation and the pileup output. Anyone know of a 
|> >better method?
|> 
|> I have extensively used the GCG program Publish for similar representations.  I
|> haven't tried it for exactly this case but it should work.  Within the Publish
|> menu, answer FCKKKKKK.....i to specify your translation first, then your novel
|> sequence, then all the other sequences, and finally a blank separator line. 
|> Make sure to specify your MSF sequences properly, e.g. Pileup.MSF{novel}.  Give
|> it a try, my users are generally quite pleased with the results.
|> 
|> 						Steve Thompson
|> 						WSU VADMS Center
|> 


Hmmm...That's exactly what I tried wanting to help Brian but found
out quickly that publish does not know how to work with MSF files.
I guess the next-best thing to do here is to ugly-fy the pileup.msf
file and use the resulting individual files -and the consensus- with
Publish. This should - if ever there are cumbersome ways of doing
things- work!

R:)

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* RODRIGO LOPEZ SERRANO  rodrigol at biotek.uio.no                           * 
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