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Notes on proposed feature display application

 Subject: Re: [EMBOSS] [BiO BB] Tool to mutate DNA
sequence
From: "Maximilian Haeussler" 
Date: Sun, February 19, 2006 1:52 pm
To: "The general forum at Bioinformatics.Org"

Cc: "bioperl-l"  (more)
Priority: Normal
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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





On Sun, Feb 19, 2006 at 02:52:37PM +0100, Maximilian
Haeussler wrote:
> 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?

Well, there is Alfresco
http://www.sanger.ac.uk/Software/Alfresco/

Guy Bottu,
Belgian EMBnet Node

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