[BioRuby] seeking advice on displaying sequence features

[Bernd Jagla]

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