Genomic Browser

Question

[spandankeshav]

Hi,

I am wondering if there would be any good genomic browser like ensemble (unfortunately, it has only eukaryotic genomes)? I am working on prokaryotic (eg. streptomyces species) and I would like to detail study of it's gene position on genome and what are other neighbour genes and what sort of functions they are doing? The neighbour ones and the gene it's are performing the same funcitons together? They are linked to each other or not? I am trying to figure these kind of questions but still not able to find any good software or browser. So, any suggestions or help will be grateful for me. Thanks a lot!

Keshav

[Pierre Lindenbaum]

"unfortunately, it has only eukaryotic genomes" wrong: http://bacteria.ensembl.org/index.html

[Michael]

"The neighbour ones and the gene it's are performing the same funcitons together?" : you are looking for functionally related gene clusters in prokaryotes: e.g. operons. Search for operon prediction.

"I am working on prokaryotic (eg. streptomyces species)" : plural implies you want to look at multiple species at once: search for "comparative genomics"

Answer 1

[Mary]

IMG can do that for you. If you access their neighborhood view, you can see gene organization in multiple species.

http://img.jgi.doe.gov/cgi-bin/w/main.cgi

Answer 2

[Ali]

Perhaps you can find your answer in this post. By google I found many: JPGV, PGV, GenColors and so on.

Answer 3

[Khader Shameer]

If your genome of interest do not have a dedicated genome browser, you can compile the annotation data that you require from multiple sources (or primary databases) and setup a local instance of GBrowse or JBrowse.