Nucleic Acids Research, 2005, Vol. 33, Database issue D86-D90
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
Agricultural Biotechnology Center, Gödöll
, Szent-Györgyi Albert u. 4, H-2100, Hungary and 1 Institute of Enzymology, Biological Research Center of the Hungarian Academy of Sciences, Budapest, Karolina út 29, H-1113, Hungary
* To whom correspondence should be addressed. Tel: +36 28 526112; Fax: +36 28 526101; Email: barta{at}abc.hu
Present address: Csaba P. Ortutay, Institute of Medical Technology, University of Tampere, F-33014 Tampere, Finland
Received August 15, 2004; Revised September 29, 2004; Accepted October 13, 2004
DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. Blanco, D. Farre, M. M. Alba, X. Messeguer, and R. Guigo ABS: a database of Annotated regulatory Binding Sites from orthologous promoters Nucleic Acids Res., January 1, 2006; 34(suppl_1): D63 - D67. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Schmid, R. Perier, V. Praz, and P. Bucher EPD in its twentieth year: towards complete promoter coverage of selected model organisms Nucleic Acids Res., January 1, 2006; 34(suppl_1): D82 - D85. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Y. Galperin The Molecular Biology Database Collection: 2005 update Nucleic Acids Res., January 1, 2005; 33(suppl_1): D5 - D24. [Abstract] [Full Text] [PDF]
|
|