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
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spandankeshav •
Thanks for the reply but @Pierre: I couldn't find any of the streptomyces species genomes on ensemble bacteria. Could you please be more specific? @Michael: I am looking for the functions of the genes which are located nearby of my own gene of interest so that I could be able to predict the functions of my gene on the basic of elucidation of the gene composition at the genetic loci.
Could you post this as a comment please and delete this answer. Now it appears as if your question was answered already.
IMG can do that for you. If you access their neighborhood view, you can see gene organization in multiple species.
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.
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"unfortunately, it has only eukaryotic genomes" wrong: http://bacteria.ensembl.org/index.html
"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"