Question

Bacterial Annotation

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12.3 years ago

Shaun ▴ 20

I am working on annotating a bacterial genome and this is my first time doing so. I got the genes in the genome but am starting to look at intergenic regions. Any suggestions on good programs for identifying RNAs and promotor sequences?

genome • 3.1k views

ADD COMMENT • link updated 4.7 years ago by Biostar 20 • written 12.3 years ago by Shaun ▴ 20

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related: http://biostar.stackexchange.com/questions/1663/identified-potential-non-coding-rna-and-then

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 12.3 years ago by Michael 54k

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and here: http://biostar.stackexchange.com/questions/6791/how-to-get-promoter-sequences-for-non-model-organisms/6918#6918

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 12.3 years ago by Michael 54k

Ram · Answer 1 · 2012-02-17

Are you planning to submit this, I'm assuming newly sequenced genome, to one of the big databases (e.g. NCBI)? If so then you should definitely ask to get access to their annotation tools [?]here[?]

Otherwise, there are quite a few tools out there. Here are some of them:

http://molbiol-tools.ca/Promoters.htm

http://linux1.softberry.com/berry.phtml (specifically [?]BPROM[?])

[?]BacPP is another one[?]

Hope this helps