Retrieving large datasets from NCBI
2
0
Entering edit mode
8.4 years ago
Naresh ▴ 60

Hi all, How to retrieve large datasets from NCBI for a particular species and then to connect NCBI database to our program so that we can get taxonomic ID of each species automatically without doing it manually.

for eg. Connect the NCBI database to Perl OR C#

Thanks Naresh

Assembly seq • 2.0k views
ADD COMMENT
1
Entering edit mode
8.4 years ago
pld 5.1k

If you plan on having very heavy access (very large queries, or many very small queries), I would just install a local copy of the NCBI taxonomy database.

Eutils asks that the query rate be no larger than 3 per second, so if you need to quickly bring up IDs for more than a few species, it probably wont work.

ADD COMMENT
0
Entering edit mode

How to install a local copy of the NCBI taxonomy database?

ADD REPLY
0
Entering edit mode

From their FTP site here.

ADD REPLY
0
Entering edit mode
8.4 years ago

It looks like what you're looking for is the eutils programs.

ADD COMMENT
0
Entering edit mode

Yes. exactly. I need to get taxonomic IDs of saccharomyces pombe. and need to connect to my C# program.,

ADD REPLY

Login before adding your answer.

Traffic: 1872 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