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Downloading all COI sequences from BOLD database

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?

bold coi barcoding
• 7,147 views • link
written by bioinfo bioinfo

1 answer

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by bioinfo bioinfo

Looks like that would work too.

• 0 views • link
written by GenoMax GenoMax

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