orthology/paralogy mapping of whole genomes - (Nov/27/2006 )

hullo ppl,

I intend to create an orthology/paralogy map of two different organisms, like an organism 'x' and another organism 'y'.

The idea that i have is that I would represent the organism 'x' s chromosome as dots and connect the dots whenever a paralog occurs. To depict the orthology of the genes with the organism Y, I would colour code the lines that network the dots. (each colour code corresponding to different chromosomes of the organism 'Y').

1.While this is one such idea, I would like to know if there would be better representations for such mapping.???

2. I have no clue as to how I should go about generating the maps???

Any help is great help.

-string-

examine the ensembl database at the ebi.

-perlmunky-

thanks perlmunky,

While the ensembl tools gave me an idea of how orthology/paralogy can be represented
the tools there look limited in a sense that one can map or position an organism 'x' s genes on template chromosomes of only a selected few organisms.

What I am looking for is however a generic way of doing the above for any two different organisms, and generating my own maps......

-string-

Hi,

I know there is an ensembl developer on another forum I admin:
http://bioinformaticsonline.co.uk/forum/

we are undergoing a few changes at the moment so the forum does not look at all great however there is someone there (provided he isn't working too hard) that should be able to give you some hints and tips should you ask nicely.

-perlmunky-

QUOTE (perlmunky @ Nov 29 2006, 05:40 AM)

There is a linux based tool called "circos" which helps in generating maps for inter genome comparsions. It looks to me a as a good tool and has got excellent representations.

http://mkweb.bcgsc.ca/circos.

However, I am having trouble working with it and will be happy to know if anyone else out there has had an experience working on it...so that I can share my queries with them....

have a good day.!!!

-string-