[Bioperl-l] [BiO BB] Tool to mutate DNA sequence

Maximilian Haeussler maximilianh at gmail.com
Sun Feb 19 08:52:37 EST 2006


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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