Question: Downloading all COI sequences from BOLD database
0
gravatar for bioinfo
7 days ago by
bioinfo740
New Zealand
bioinfo740 wrote:

Hi all,

Is there a way to download all COI sequences from BOLD database (http://www.boldsystems.org/index.php/Public_SearchTerms)? I tried to download all sequences from the search button of "Public Data Portal" without any search term but it returns zero hits.

I also tried with a search term of "Arthorapoda" which actually returned

Found 4,791,963 published records,
with 4,791,963 records with sequences,
forming 402,549 BINs (clusters),
with specimens from 243 countries,
deposited in 1,566 institutions.

Of these records, 2,282,392 have species names, and represent 200,331 species.

With download options on the top right.

I was thinking if any of you have used a better option such as API or via command line to download all COI sequences?

barcoding coi bold • 73 views
ADD COMMENTlink modified 7 days ago • written 7 days ago by bioinfo740
0
gravatar for genomax
7 days ago by
genomax70k
United States
genomax70k wrote:

Looks like entire data file is available in tsv format here. This is the latest Dec 31, 2015 release.

ADD COMMENTlink modified 7 days ago • written 7 days ago by genomax70k

It seems the TSV file contains only a set of plant sequences (rbcL and some matK, n=1900 sequences) from 2015 release.

ADD REPLYlink written 7 days ago by bioinfo740

I am thinking the API solution such as below will do the job. I'm testing it now.

wget http://v3.boldsystems.org/index.php/API_Public/sequence?marker=COI-5P

More info are available here about API http://v3.boldsystems.org/index.php/resources/api?type=webservices#sequenceParameters

ADD REPLYlink written 7 days ago by bioinfo740

Looks like that would work too.

ADD REPLYlink written 7 days ago by genomax70k

There are many other release here. You may need to look through them.

ADD REPLYlink written 7 days ago by genomax70k
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: 1319 users visited in the last hour