Question: get gene annotation for nucleotide sequence of the NCBI RefSeq database
0
gravatar for dabid
5 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 • 344 views
ADD COMMENTlink modified 5 months ago • written 5 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 5 months ago by h.mon9.8k

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 5 months ago by dabid0
1
gravatar for dabid
5 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 5 months ago by dabid0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1387 users visited in the last hour