Sequence alignment documentation

burglin at ubaclu.unibas.ch burglin at ubaclu.unibas.ch
Mon Sep 2 02:45:26 EST 1996


In article <cas9-2108961128480001 at 128.84.203.131>, cas9 at cornell.edu (Claudia Sutton) writes:
> 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  
>>  ------------------------------------------------------------------------

Actually, I am useing a lineup with no boxes,
then I import the sequence into Mac MacDrawPro (
print setting set to "precise text" in preferences).
when you use Courier 10, or Courier 12,  the
characters match exactly on the inch, i.e. 10 gives 
12 characters per inch, size 12 gives 10 characters
per inch.  Then you set the grid to 24 divisions,
and nudge the letters to conincide with the grid.
Then you turn on the grid, and the boxes will now
neatly snap between the letters (at half letter
distances, so you have some leaway in the vertical
direction, since you can't set that seperatly).

Thomas Burglin









More information about the Bio-soft mailing list