[Taxacom] Specimen database that works with sequence data

Alex Borisenko aborisen at uoguelph.ca
Fri Nov 14 11:08:24 CST 2014


Hi Eric, 
If you are looking for COI, you can perform this search on the Barcode of Life Data Systems (www.boldsystems.org). 
Go to http://v3.boldsystems.org/index.php/Public_BINSearch?searchtype=records 
Then type "united states"[geo] insecta[tax] (or whatever other taxon you are searching for) in the search string. 
Once the search is complete, you can download the FASTA file by clicking the corresponding menu icon. 

For a more refined search or to run analyses, you would have to create a BOLD user account (free) and run the search when you are logged on. 
You can also use BOLD to manipulate your own data if you are willing to submit them. 

Hope this helps. 

Best wishes 
Alex 



From: "Eric Chapman" <ericgchapman at gmail.com> 

To: taxacom at mailman.nhm.ku.edu 
Sent: Thursday, November 13, 2014 2:35:00 PM 
Subject: [Taxacom] Specimen database that works with sequence data 

Hello, 

I was wondering if anyone could tell me if there is a database available 
that houses both collection information and DNA sequences of multiple 
genes such that I could query that database in this way: 

For all specimens that are from the US with COI sequences, give me a FASTA 
(or other DNA format) file containing all of the sequences. 

I don't care if the sequences are aligned - I can do that part. I have been 
working with a data file and selecting a subset of sequences by hand in 
MacClade or Mesquite, which has become very time consuming as the data set 
has grown to well over 1000 sequences. I am not skilled at writing scripts, 
so extracting them that way is not practical for me. I have never used 
Sequencher - does it have this capability? 

I would appreciate any input any of you can give me. 

Regards, 
Eric Chapman 

-- 
Eric G. Chapman, PhD 
Research Analyst, Collections Manager 
Department of Entomology 
University of Kentucky 
S225 Agricultural Science Center N 
Lexington KY 40546-0091 USA 
(859) 257-3169 (lab) 
(330) 221-7812 (mobile) 
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