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get gene annotation for nucleotide sequence of the NCBI RefSeq database

I have fasta files of different genomes of bacteria taken from the NCBI RefSeq database. I want to get the annotation of these genomes as the ones that can be shown in the genbank file format. What I mean by annotation is cds (gene start/end positions, description, and others). Anyway, I want to extract cds (nucleotide sequence) that have title/description of prophages.

gene ncbi annotation cds dna
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written by dabid • dabid

Where did you download the fastas? Could you give an example? In general, you will find the annotation on the same folder you found the fastas.

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written by h.mon h.mon

As I mentioned, I downloaded these fasta files from NCBI (RefSeq database). I just to know that genbank files have such information. But don't know how to extract the genbank files specific to my downloaded fasta files

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written by dabid • dabid

1 answer

Maybe it is not an exact answer for my question, but as a turn around, what I needed doing is downloading the bacteria genomes that I need from the NCBI RefSeq database as a genbank files. Then, it's easy to process these genbank files using Biopython library to get CDs, etc.

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written by dabid • dabid

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