[Taxacom] Specimen database that works with sequence data

Urmas Kõljalg urmas.koljalg at ut.ee
Fri Nov 14 09:57:06 CST 2014


 

Hi, 

PlutoF cloud (http://plutof.ut.ee ) provides such services where you can
develope combined datasets of different taxon occurrences (including
specimen and DNA data). Sequence data can be downloaded as a Fasta file
through the Clipboard system provided by the online workbench. Probably
most well known such dataset hosted by PlutoF is UNITE fungal rDNA ITS
database (http://unite.ut.ee ) which is utilized by many NGS pipelines
like QIIME, mothur, SCATA, UTAX, etc. 

Best wishes, 

Urmas Kõljalg 

13-11-2014 14:35 kirjutas Eric Chapman: 

> 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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