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publication-quality protein alignments

Michele Clamp michele at speed.ebi.ac.uk
Tue May 12 09:23:00 EST 1998


Ewan Birney <birney at sanger.ac.uk> writes:

> Jonathan Epstein wrote:
> > 
> > I am looking for some software to produce attractive proteins alignments
> > suitable for publication.  It possible, this software should run on a
> > Macintosh or a Web-based platform.
> >
> 
> Hmmm. There is a non-obvious set of choices - including
> 
> 	Seaview  (biom3.univ-lyon1.fr - ftp - unix)
> 	alscript (-C program - makes ps. barton.ebi.ac.uk) 
> 	genedoc (windows NT)
> 	belvu (I like it... ftp://ncbi.nlm.nih.gov/pub/esr/ - unix)
> 
> As for pure Web based ones, I know of one java alignment viewer...
> but sadly unreleased yet... ;(

Hmm I think he may mean Jalview.  No it isn't released yet (soon 
to be beta) but if some intrepid souls wish to try it out you can 
have a look at its home page

http://circinus.ebi.ac.uk:6543/jalview/

and trial applets are at

http://circinus.ebi.ac.uk:6543/jalview/try.html
and
http://circinus.ebi.ac.uk:6543/jalview/groups.html

I don't know if the output will be exactly what you want - 
postscript is generated and mailed back to you.  For real
flexibility (but ahem a not overfriendly interface :) alscript 
does the job.  (I should declare an interest here as I work
in Geoff Barton's group.)

Cheers

Michele.
-- 
Dr Michele Clamp ,        EMBL-European Bioinformatics Institute 
Hinxton, Cambs CB10 1SD,  email : michele at ebi.ac.uk
UK                        Tel:  01223 494682    Fax: 01223 494468




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