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DoOP - Databases of Orthologous Promoters


NAR Molecular Biology Database Collection entry number 663
Barta E.1, SebestyÉn E.1, PÁlfy T.B.1, TÓth G.1, Ortutay C.P.1 and Patthy L.2
1Agricultural Biotechnology Center, GÖdÖll?, Szent-GyÖrgyi Albert u. 4, H-2100, Hungary
2Institute of Enzymology, Biological Research Center of the Hungarian Academy of Sciences, Budapest, Karolina Út 29, H-1113, Hungary
Contact barta@abc.hu

Database Description

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 21061 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.

This work was supported by Biotechnology 2001 grant BIO-0117/01 from the Central Technical Development Target Funds (Hungary). B.E. and G.T. were recipients of 'Bolyai Fellowship’ awarded by the Hungarian Academy of Sciences.


Go to the abstract in the NAR 2005 Database Issue.
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