[BioRuby] seeking advice on displaying sequence features

[jan aerts (RI)]

Hi Bernd.

Good to hear that people are flocking around ruby and bioruby.

The Bio::Graphics module (that integrates with bioruby) does part of the job that you want to do. Have a look at http://bio-graphics.rubyforge.org That website will give you an idea of the type of picture you can generate. At the moment, it does only that: generate the picture. There is no interactivity available yet apart from making it possible to create clickable glyphs (if you open the picture in a web browser).

I think part of the things you want to do would involve a Rails application. I do have a proof-of-concept working (was pretty easy), but there is no release or something of a Rails-based tool that uses Bio::Graphics.

I hope this can help you a bit further.

If you've got any more questions, just let the mailing list know...

jan.


-----Original Message-----
From: bioruby-bounces at lists.open-bio.org on behalf of Bernd Jagla
Sent: Fri 26/10/2007 14:14
To: bioruby at lists.open-bio.org
Subject: [BioRuby] seeking advice on displaying sequence features
 
Hi,

 

I am new to Ruby and BioRuby. And I want to learn both!

 

For me the best way of doing this is a little project. I would like to get
some pointers and suggestions from you on how to do this and where to start.

Maybe it has already been done..

 

Anyways, here is what I want to do:

 

I have a list of nucleotide sequences (genomic) and a list of features
(introns, exons, TFBS, ECRs, etc), basically information in the form

Property; start; end; ?direction?

AND

Just the sequence

AND

Gene/sequence name(s), description, comments

 

Now I want to display those properties in at least two different ways:

1.	all sequences in parallel lines (length correlates with sequence
length) and features are color coded objects plotted on top of those lines
2.	sequence with boxes, underlined or otherwise marked regions

 

I probably need the ability to zoom, mark, and select specific sequence
regions

I would like to manually align or move the sequences around based on some
user defined marker

I want to be able to select the properties to show and export those selected
properties in a variety of formats.

 

I hope, I described the problem sufficiently to allow anyone to give me some
advice on where to start, if someone has already done parts of that, and
probably a list of function I should be using etc. I would be happy to
contribute the final code to the community, if there is interest..

 

Thanks for your kind help and interest,

 

Regards,

 

Bernd

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