Genome assembly

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3.0 years ago

netipandey.87 ▴ 10

I have downloaded 30 complete genome assemblies of a bacteria. I want to perform a 16s Rna genetic analysis.. I can extract the sequence manually...however...I came across contest16s... Now my...question is..can I extract the 16s sequence of all 30 genomes together at a single go by using contest16s.. Or can you suggest any other web based software for doing the same.. Thanks and Regards...

assemblies Genome • 1.0k views

ADD COMMENT • link updated 3.0 years ago by GenoMax 141k • written 3.0 years ago by netipandey.87 ▴ 10

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Where did you download the genomes from? Available genomes are usually annotated, in PATRIC and NCBI for instance there are .frn files with the predicted RNA genes and you can easily extract the ssuRNA from them.

ADD REPLY • link 3.0 years ago by Asaf 10k

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please fix your title, this question is not about genome assembly but extracting sequences

ADD REPLY • link 3.0 years ago by Istvan Albert 100k

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can I extract the 16s sequence of all 30 genomes together at a single go by using contest16s

What is contest16s? Consensus 16S?

If you are looking for methods to do this then see this paper. Basically you are going to be doing blast searches with your genomes against an appropriate database.

ADD REPLY • link 3.0 years ago by GenoMax 141k

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