DOOR: A prokaryotic operon database for genome analyses and functional inference

Huansheng Cao, Qin Ma, Xin Chen, Ying Xu

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

The rapid accumulation of fully sequenced prokaryotic genomes provides unprecedented information for biological studies of bacterial and archaeal organisms in a systematic manner. Operons are the basic functional units for conducting such studies. Here, we review an operon database DOOR (the Database of prOkaryotic OpeRons) that we have previously developed and continue to update. Currently, the database contains 6 975 454 computationally predicted operons in 2072 complete genomes. In addition, the database also contains the following information: (i) transcriptional units for 24 genomes derived using publicly available transcriptomic data; (ii) orthologous gene mapping across genomes; (iii) 6408 cis-regulatory motifs for transcriptional factors of some operons for 203 genomes; (iv) 3 456 718 Rho-independent terminators for 2072 genomes; as well as (v) a suite of tools in support of applications of the predicted operons. In this review, we will explain how such data are computationally derived and demonstrate how they can be used to derive a wide range of higher-level information needed for systems biology studies to tackle complex and fundamental biology questions.

Original languageEnglish (US)
Pages (from-to)1568-1575
Number of pages8
JournalBriefings in bioinformatics
Volume20
Issue number4
DOIs
StatePublished - Mar 27 2018

Keywords

  • DOOR
  • gene regulation
  • genomic organization
  • operon database
  • transcription unit

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

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