annotation with prokka

morning latte

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annotation with prokka

01-01-2014, 10:26 AM

Hello world,

This would be a silly question but could someone help me understand what prokka is doing? As far as I know, I can use assembled config fasta file to blast. For example, if I have bacterial nucleotide sequence, I can use blatx program then my nucleotide sequence is converted to protein sequences and they are searched through protein database in genbank. It is said that prokka output could be used for genbank submission. Why do we want to use prokka? Any comment would be greatly appreciated.
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boetsie

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Join Date: Feb 2010

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01-01-2014, 11:02 AM

Prokka is a pipeline to predict genomic elements, such as genes, rRNA, tRNA and non-coding RNA. In addition, it annotates the genes with BLAST against the swissprot database and other databases. Prokka generates files that can directly be used for submission in GenBank.

Regards,
Boetsie
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morning latte

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01-02-2014, 01:50 PM

Dear boetsie,

Thanks a lot!
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