[Taxacom] Specimen database that works with sequence data

Eric Chapman ericgchapman at gmail.com
Thu Nov 13 13:35:00 CST 2014


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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