how can I search for Attachment sites in my bacterial genome

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6.7 years ago

Optimist ▴ 180

Hello all,

I'm trying to explore the genomic wide composition of a multidrug resistant bacteria.

As part of this project I'm trying to detect the presence of Integrative and conjugative elements (ICEs) in my genome. Attachment sites are the characteristic features of ICEs, so i'm trying to locate the presence of att sites which may in-turn locate ICEs in my genome.

Can someone over here help me (with either tools or relevant literature) in finding the presence of att sites in my genome.

Can someone list out the sequences of various att sites (like attP and attB)?

Thanks a lot

Cheers

Optimist

att ICE HGT MDR bacteria • 1.4k views

ADD COMMENT • link updated 6.5 years ago by baroyahya • 0 • written 6.7 years ago by Optimist ▴ 180

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Do you have a database or reference set of the att sites you're interested in? If so, just blasting them all against your genomes of interest is the simplest solution.

ADD REPLY • link 6.7 years ago by Joe 21k

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I don't have any database related to att sites of bacteria.

Can you please provide me the links to any of the att sites databases that you are aware of.

Thanking You

Optimist

ADD REPLY • link 6.7 years ago by Optimist ▴ 180

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Have you any evolution about your work since your last post?

ADD REPLY • link 6.5 years ago by baroyahya • 0

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