publication quality alignments w/Motifs?

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Tue Mar 9 10:25:38 EST 1999

In article <36E534B7.ACAB0E8D at nih.gov>,
	Jonathan Epstein <Jonathan_Epstein at nih.gov> writes:
> Hi,
> What do people out there use for producing publication-quality multiple
> alignments?


> In particular, I need to highlight some Motifs, and also should some
> discontinuity in some of the sequences, where I don't want to show
> hundreds of residues of uninteresting sequence.

	I'm editing the .blc before running alscript to remove unwanted
	sequences and add "<nb of residues deleted>".

	You can find an example in :

Jeanmougin F, Wurtz JM, LeDouarin B, Chambon P, Losson R 
The bromodomain revisited 
Trends Biochem Sci 1997;Vol 22, Iss 5:151-153 

	There waas a GUI for alscript but I prefer "vi" or writing the
	suitable script. Ho, yes, it's scripting, but it does what you attempt
	to (WYGIWYG).

> I have a PC on my desk, and have access to numerous Unix hosts,
> including one using GCG.  In a pinch, I can use a Mac running MacVector.

	alscript produces high quality postscript output.

> I need to get these diagrams out quickly, so am especially interested in
> freeware and/or time-bombed demos.

	should be fast, just check alscript home page.

> I understand that Vector NTI is pretty well thought of these days for
> Windoze users.  Does the demo version have the sorts of capabilities
> which I mention?


François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

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