Hi Maximilian,

    I hope that I understand your question. An easy way to do so is to
put your sequences in a separate arrays, loop overs these arrays while
comparing positions, if the nuc/aa are equal, then push a pipe  ( "|" )
in a third separate array, else push a space ( " " ). Once it's done,
print your arrays by looping over them...


array1 qw (A A G C T)
array2 qw (C A C C G)
array3 qw (  |   |  )

Then, print your arrays and that will give you

A A G C T
  |   | 
C A C C G

Surely, you can color whatever you want in that case too (i.e : the aligned nuc).



Hope this was clear

Pierre



On Sun, 2006-02-19 at 14:52 +0100, Maximilian Haeussler wrote:

> Hi bio-mailinglists,
> 
> does anyone here know of a tool or a library to display two (or more)
> sequences at the same time with coloured features? Possibly with lines,
> connecting some features from one sequence to the other (synteny-plot) ?
> Or to display two multiple alignments, one on top of each other, with
> colored features added?
> 
> It's not that it would be difficult to write, but programming visualisation
> usually takes a lot of time.
> Bio::Graphics seems mainly concerned with one main sequence and features on
> it. Well, I could copy together two of these gif-images, but then there
> would be no connecting lines. Same applies for the graphics in Biojava or
> the gff2ps tool or all the multiple alignment viewers that I know (Bioedit,
> ClustalX). There is something called Toucan in Java, which displays at least
> several lines of gff-style-features, but no visible sequences and more
> importantly, no connecting lines. A recent software, Djinn lite, is using a
> similar kind of visualization to compare different spliced genes from
> various species, but it's mainly aimed at splicing and written in Visual
> Basic.
> I guess a good compromise might be the 3D viewer Sockeye, but I haven't seen
> any synteny-lines in sockeye yet.
> 
> I guess I must have missed something here. I cannot be the first one that
> would like to compare, say, two gff files, or two multiple alignments?
> 
> Thanks a lot for any idea,
> Max
> 
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