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-   -   annotation with prokka (http://seqanswers.com/forums/showthread.php?t=39579)

morning latte 01-01-2014 10:26 AM

annotation with prokka
 
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.

boetsie 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

morning latte 01-02-2014 01:50 PM

Dear boetsie,

Thanks a lot!


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