Sequence alignment documentation

Claudia Sutton cas9 at cornell.edu
Wed Aug 21 05:28:48 EST 1996


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  
>  ------------------------------------------------------------------------




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