Representing A Feature Along The Length Of The Chromosome

Question

[arunbhupathy]

i have a list of Plasmodium vivax genes with their chromosomal location.I want to represent these genes as a colored bar plotted along the chromosome like in this figure.Can anyone please help me in this regard....

[Pierre Lindenbaum]

highly similar to : http://www.biostars.org/post/show/378/

Answer 1

[bernatgel]

Answering after a few years, in case anyone comes to this question from google et al.

You can use karyoploteR to plot almost anything on any genome. There are some examples in the karyoploteR page including one on plotting genes on a P Vivax genome from PlasmoDB.

Answer 2

[Maxime Lamontagne]

Stripe software: http://bioinfo.mikrobio.med.uni-giessen.de/wiki/index.php/Stripe

Article describing the software: http://www.biomedcentral.com/1471-2105/7/348

[arunbhupathy]

Thank u........................................

Answer 3

[Christian]

If you specifically want to do this for a Plasmodium genome, you could try a recently added feature in PlasmoDB 9.0.

When you do a gene search in PlasmoDB, you will find a tab at the top of your result list saying "Genome View (beta)". When you click on it, it will show you the location of your genes along the chromosomes. Obviously this approach only works if you can formulate a meaningful query for your genes of interest.

Here is one example produced by searching for P. vivax "polymerase":