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Protocols

diArk specifications

Information


Unique identifier OMICS_03332
Name diArk
Restrictions to use None
Version 3.0
Maintained Yes

Maintainer


  • person_outline Martin Kollmar

Publications for diArk

diArk citations

 (5)
library_books

Exploring Neighborhoods in the Metagenome Universe

2014
Int J Mol Sci
PMCID: 4139848
PMID: 25026170
DOI: 10.3390/ijms150712364

[…] verse, all archaeal, bacterial and viral genomes were downloaded from the National Center for Biotechnology Information (NCBI) FTP server [,]. They were complemented by 53 Eukaryotic genomes, 33 from diArk [] and 20 from NCBI. As described in [], we also included virus-enriched metagenomes to manage the underrepresentation of viral diversity in genome databases. For each reference, the Pfam profil […]

call_split

The nuclear F actin interactome of Xenopus oocytes reveals an actin bundling kinesin that is essential for meiotic cytokinesis

2013
PMCID: 3981176
PMID: 23727888
DOI: 10.1038/emboj.2013.108
call_split See protocol

[…] The kinesin genes have been identified by TBLASTN and PSI-BLAST searches against the sequenced eukaryotic genomes, which have been obtained via lists available from the diArk database (). All hits were manually analysed at the genomic DNA level together with the multiple sequence alignment of all kinesin proteins to reveal homologous regions. If available for a given […]

library_books

A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem coronin, defines a new subfamily, and predicts protein function

2011
BMC Evol Biol
PMCID: 3203266
PMID: 21943019
DOI: 10.1186/1471-2148-11-268

[…] searches against the corresponding genome data of the different species. The list of sequenced eukaryotic species as well as access information to the corresponding genome data has been obtained from diArk []. Species that missed certain orthologs in the first instance were later searched again with supposed-to-be orthologs of other closely related species. In this iterative process all coronin fa […]

call_split

WebScipio: An online tool for the determination of gene structures using protein sequences

2008
BMC Genomics
PMCID: 2644328
PMID: 18801164
DOI: 10.1186/1471-2164-9-422
call_split See protocol

[…] tion is implemented in the Ruby programming language [] using the Ruby on Rails [] framework. The list of the genome files available for search are stored in an index file which is generated from the diArk database []. We are searching for new releases of genome data on a weekly basis, and as soon as new data is released it will be available to WebScipio. The index file contains metadata about the […]

library_books

The Molecular Biology Database Collection: 2008 update

2007
Nucleic Acids Res
PMCID: 2238887
PMID: 18025043
DOI: 10.1093/nar/gkm1037

[…] However, this task is carried out by much more comprehensive listings in the GOLD database [http://www.genomesonline.org/, no. 75, ()] and Entrez Genomes web site [no. 458, ()]. The recently created diArk database [http://www.diark.org/diark/, no. 1172, ()] lists eukaryotic genome sequencing projects. Several more databases have been superseded by more advanced or more comprehensive databases. Fo […]

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diArk institution(s)
Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

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