IUBio

MSF representations for publication

Steve Thompson: VADMS genetics THOMPSON at JAGUAR.CSC.WSU.EDU
Thu May 26 10:17:18 EST 1994


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




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