refseq NC id list download
2
0
Entering edit mode
6.1 years ago

hello i have a list of genes with their nc ids is it posible to download the bulk list from refseq database Thanks

refseq gene genomics ncbi • 2.6k views
ADD COMMENT
1
Entering edit mode
6.1 years ago
#### ▴ 220

May be you can try NCBI Entrez http://www.ncbi.nlm.nih.gov/sites/batchentrez

ADD COMMENT
0
Entering edit mode

Works pretty well, although with >10,000 entries you might be obliged to split queries (you might get a "bad gateway" error). My longest download consisted of slightly more than 5000 entries.

ADD REPLY
0
Entering edit mode
6.1 years ago
GenoMax 115k

If you have access to refseq blast databases from NCBI then you can use blastdbcmd to extract the sequence (if that is what you are after).
Other option could be e-utilities from NCBI.

ADD COMMENT
0
Entering edit mode

Sir, i tried this but its not working for me . any other option to download bulk of NC ids

ADD REPLY
0
Entering edit mode

Can you be more specific about what is "not working"? Perhaps we can debug that part.

ADD REPLY
0
Entering edit mode

I have a list of NC ids of genes of interest , i want to download them into a single shot . so that i dnt need to go for individually download

ADD REPLY
0
Entering edit mode

You had already said that in the original post.
The blastdbcmd method should work in this case. If you tried to use that and ran into some problems then let us know what did not work with that method.

ADD REPLY

Login before adding your answer.

Traffic: 1693 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6