DoOp: Databases of orthologous promoters, collections of clusters of orthologous upstream sequences from chordates and plants

E. Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, L. Patthy

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

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.

Original languageEnglish
JournalNucleic Acids Research
Volume33
Issue numberDATABASE ISS.
DOIs
Publication statusPublished - Jan 1 2005

Fingerprint

Chordata
Databases
Exons
Conserved Sequence
Viridiplantae
Transcription Initiation Site
Multigene Family
Arabidopsis
Genes
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

DoOp : Databases of orthologous promoters, collections of clusters of orthologous upstream sequences from chordates and plants. / Barta, E.; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, L.

In: Nucleic Acids Research, Vol. 33, No. DATABASE ISS., 01.01.2005.

Research output: Contribution to journalArticle

Barta, E. ; Sebestyén, Endre ; Pálfy, Tamás B. ; Tóth, Gábor ; Ortutay, Csaba P. ; Patthy, L. / DoOp : Databases of orthologous promoters, collections of clusters of orthologous upstream sequences from chordates and plants. In: Nucleic Acids Research. 2005 ; Vol. 33, No. DATABASE ISS.
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