Question: How To Study The Characteristics Of Neighboring Genes (Of A Query) Of A Bacterial Species?
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gravatar for spandankeshav
7.0 years ago by
Finland
spandankeshav80 wrote:

Hi, I am trying to analyze the function of certain genes along with the predefined characteristics (if any), which locates nearby of the query gene (neighboring genes may be 5 genes forward and backwards necessarily from the query) of bacteria species (mainly streptomyces species) in a whole genome. Is there any browser/software to perform this task? I have noticed NCBI genomic browser but didn't find any relevant information regarding what I am looking for as most of the genes allocated are not reviewed (so lack of information)....Any suggestion/views would be great! Thanks! -Spandan

genes • 2.1k views
ADD COMMENTlink modified 7.0 years ago by Alex Reynolds31k • written 7.0 years ago by spandankeshav80

Is your question how to efficiently get a program to find the 5 genes in front/behind each gene in the strep. genome, how to assess the function of those genes, or both?

ADD REPLYlink written 7.0 years ago by Devon Ryan97k

Actually, Both!

ADD REPLYlink written 7.0 years ago by spandankeshav80

The first part is "relatively easy" with GenomicRanges, though I've never tried to use that on a circular genome (I think there's support for that). Of course, you'd need an annotation (GTF or GFF, normally) for the genome, which I presume exists.

For the functional annotation part, I guess it's a question of whether there are already gene ontology mappings for strep. and if that's sufficient for your needs (I obviously don't work on prokaryotes, so I don't know what else might be out there for them). If you have something else in mind, then you might update your question to mention that.

If that turns out to be exactly what you need (well, it gets you the information, what you do with it from there is up to you), then first start playing around with GenomicRanges in R to see if you can get it working properly. You can then update your question (or close it and post a new one if that makes more sense) with more precise questions about the various steps that you're trying to perform.

ADD REPLYlink written 7.0 years ago by Devon Ryan97k

Have you tried: http://microbes.ucsc.edu

ADD REPLYlink written 7.0 years ago by microbeatic80
2
gravatar for Alex Reynolds
7.0 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

ADD COMMENTlink modified 10 months ago by RamRS30k • written 7.0 years ago by Alex Reynolds31k
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