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DoOP specifications

Information


Unique identifier OMICS_20937
Name DoOP
Alternative name Database of Orthologous Promoters
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Content license Other
Maintained No

Subtool


  • DoOPSearch

Maintainers


This tool is not available anymore.

Publications for Database of Orthologous Promoters

DoOP citations

 (4)
library_books

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

2012
BMC Genomics
PMCID: 3564944
PMID: 23228284
DOI: 10.1186/1471-2164-13-688

[…] s may harbor functional binding sites. However, we still observed a bias in the number of applications exclusively implemented towards the characterization of promoter sequences (e.g. TFMExplorer [], DoOPSearch [], COTRASIF [], Mapper [], CoreTF [], and Pscan [], see Table ). For this reason, tools such as CBS or GenomeSurveyor [], which allow users to conduct virtual screenings on the full sequen […]

library_books

A mutation degree model for the identification of transcriptional regulatory elements

2011
BMC Bioinformatics
PMCID: 3228546
PMID: 21708002
DOI: 10.1186/1471-2105-12-262

[…] that are listed in Table . The background sequences are from the promoters of Arabidopsis genome excluding the co-expressed genes. The phylogenetic promoters were retrieved from the plant database of DoOP (version 1.5) []. Their background sequences, i.e. the neutral sequences, or referred as a set of phylogenetically unrelated promoters, were built by sampling 100 promoters randomly from its corr […]

library_books

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

2009
BMC Bioinformatics
PMCID: 2697632
PMID: 19534734
DOI: 10.1186/1471-2105-10-S6-S1

[…] brates; by the work of Rubino and Attimonelli [], who present a new algorithm for the classification of sequences based on regular expression syntax; and by the work of Sebestyén et al. [] presenting DoOPSearch, a web-based tool using the comparative analysis of a large number of orthologous promoter regions to find common conserved motifs in the promoter regions of different chordate and plants g […]

library_books

EPD in its twentieth year: towards complete promoter coverage of selected model organisms

2005
Nucleic Acids Res
PMCID: 1347508
PMID: 16381980
DOI: 10.1093/nar/gkj146

[…] a. HemoPDB () is a more specialized resource for promoters of genes of the hematopoietic system, providing information on transcription factor binding sites in addition to TSS annotation. OMGProm (), DoOP () and CORG () are databases of orthologous promoters with a comparative genomics focus.A detailed description of the contents and format of EPD was given in Ref. (). Information about interfaces […]

Citations

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DoOP institution(s)
Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary; Bioinformatics Group, Agricultural Biotechnology Center, Godollo, Hungary; Department of Molecular Biophysics (B020), German Cancer Research Center (DKFZ), Heidelberg, Germany; Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
DoOP funding source(s)
Supported by grants from the Hungarian Scientific Research Fund (OTKA) (NK60352 and NK72730), the Hungarian Ministry of Agriculture and Rural Developmen R&D grant and the Bolyai Janos Scholarship.

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