[Taxacom] Specimen database that works with sequence data
g.droege at BGBM.ORG
Fri Nov 14 10:27:55 CST 2014
GGBN (Global Genome Biodiversity Network, http://www.ggbn.org) is providing a shared portal for DNA and tissue collections. We are currently working on the new data portal (release planned 11/2015).
Currently you can search for specimens/tissue/DNA and NCBI/BOLD numbers (see http://data.ggbn.org). In the new portal one can also search for e.g. show me specimens/samples with COI sequence. I could think of crosslinks to sequence portals to enable user e.g. to download fasta from vouchered sequences only via NCBI web services.
So GGBN focuses on available information for samples and specimens deposited in Natural History Collections. We hope to increase the percentage of vouchered sequences by getting all of our partner collections online.
It might be worth to have a look at GGBN and keep those upcoming features in mind. Any feedback and ideas are welcome.
Technical Manager - Global Genome Biodiversity Network (GGBN)
Berlin-Dahlem DNA Bank
Women's Officer ZE BGBM
Botanic Garden and Botanical Museum Berlin-Dahlem
Freie Universität Berlin
+49 30 838 50 139
Von: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] Im Auftrag von Urmas Kõljalg
Gesendet: Freitag, 14. November 2014 16:57
An: taxacom at mailman.nhm.ku.edu
Betreff: Re: [Taxacom] Specimen database that works with sequence data
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.
13-11-2014 14:35 kirjutas Eric Chapman:
> 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.
> 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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