Converting Integrated Microbial Genome (IMG) numbers to corresponding gene names/numbers

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8.6 years ago

matthew.wipperman ▴ 10

I am interested in writing a script to convert Integrated Microbial Genome (IMG) numbers to a different type of identifier, like an NCBI accession number (e.g., the WP_ or YP_ identifiers for proteins). I am unable to figure out a way to match these numbers to their corresponding genes/proteins. Any advice would be most welcome.

Thank you!

genome gene • 2.3k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 8.6 years ago by matthew.wipperman ▴ 10

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Have you had any success yet?

ADD REPLY • link 6.3 years ago by vishwaas1704 ▴ 30

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You could do this via BLAST if you have the sequences.

ADD REPLY • link 6.3 years ago by Joe 21k

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Could you explain how?

ADD REPLY • link 2.2 years ago by JMMM ▴ 10

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Download sequences with the relevant IMG identifiers. Blast each of these sequences against the NCBI database of choice (protein/nuccore/nr etc). Then you can match the sequences to the accessions etc via the actual sequence itself.

ADD REPLY • link 2.1 years ago by Joe 21k

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