Sequence alignment documentation

Francois Coulier coulier at infobiogen.fr
Thu Aug 22 01:27:00 EST 1996


On Wed, 21 Aug 1996, Claudia Sutton wrote:

> In article <32142189.A7B at bbsrc.ac.uk>, Andy Phillips
> <andy.phillips at bbsrc.ac.uk> wrote:
> 
> > o.gallay at ic.ac.uk wrote:
> > > 
> > > Hi.
> > > Does anyone out there know of a program that will draw a frame around
> > > homologous segments of sequence in alignments, ie. like "prettybox" but
> > > without the shading?  I've often seen this sort of frame in
> publications, but
> > > everyone I know thinks this has to be done by hand.
> > > Please e-mail as well as post!
> > > 
> > 
> > Genedoc (available from http://www.cris.com/~ketchup/genedoc.shtml) will
> output a 
> > lineup in PICT format, which can (theoretically) be imported into
> drawing packages. You 
> > can then draw your own boxes around conserved regions. In practise,
> however, I found 
> > that CorelDraw6 failed to align the characters properly, and Freelance
> crashed on 
> > importing large lineups. <sigh>
> > 
> > Andy
> >  ------------------------------------------------------------------------
> >  Email  : andy.phillips at bbsrc.ac.uk  : University of Bristol
> >  Home   : andy at cycad.demon.co.uk     : IACR Long Ashton Research Station 
> >  Phone  : +44-1275-549257            : Long Ashton
> >  Fax    : +44-1275-394281            : Bristol, BS18 9AF, UK
> >  WWW    : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html
> 
> 
> 
> I have been using gcg pretty outputs that I import into MS word as a
> picture, then you can draw boxes, arrows, etc.  That way seems fairly
> WSYWYG, unlike trying any of the other drawing programs.  It is however,
> fairly crude. Good luck,
> 
> Claudia Sutton
> aka cas9 at cornell.edu  
> >  ------------------------------------------------------------------------
> 
> 
Another way is to import the alignment into microsoft excell (you need to 
add a recognizable character, such as a semicolon, between each base or 
amino acid). then boxing is fairly easy, with or without shading. The 
important point is to have each base in a cell, so that the alignment 
will be independent of the font (proportional or not) used.


Francois Coulier
INSERM Unite 119
27 bd Lei Roure
13009 Marseille
France

tel (33) 91 75 84 11
fax (33) 91 26 03 64
email: coulier at infobiogen.fr





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