Question: get gene annotation for nucleotide sequence of the NCBI RefSeq database
0
gravatar for dabid
12 months ago by
dabid0
dabid0 wrote:

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.

dna cds annotation ncbi gene • 625 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by dabid0

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.

ADD REPLYlink written 12 months ago by h.mon16k

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

ADD REPLYlink written 12 months ago by dabid0
1
gravatar for dabid
12 months ago by
dabid0
dabid0 wrote:

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.

ADD COMMENTlink written 12 months ago by dabid0
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