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

Publication ,  Journal Article
Cao, H; Ma, Q; Chen, X; Xu, Y
Published in: Briefings in Bioinformatics
July 19, 2019

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.

Duke Scholars

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Published In

Briefings in Bioinformatics

DOI

EISSN

1477-4054

ISSN

1467-5463

Publication Date

July 19, 2019

Volume

20

Issue

4

Start / End Page

1568 / 1577

Publisher

Oxford University Press (OUP)

Related Subject Headings

  • Bioinformatics
  • 0899 Other Information and Computing Sciences
  • 0802 Computation Theory and Mathematics
  • 0601 Biochemistry and Cell Biology
 

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Cao, H., Ma, Q., Chen, X., & Xu, Y. (2019). DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings in Bioinformatics, 20(4), 1568–1577. https://doi.org/10.1093/bib/bbx088
Cao, Huansheng, Qin Ma, Xin Chen, and Ying Xu. “DOOR: a prokaryotic operon database for genome analyses and functional inference.” Briefings in Bioinformatics 20, no. 4 (July 19, 2019): 1568–77. https://doi.org/10.1093/bib/bbx088.
Cao H, Ma Q, Chen X, Xu Y. DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings in Bioinformatics. 2019 Jul 19;20(4):1568–77.
Cao, Huansheng, et al. “DOOR: a prokaryotic operon database for genome analyses and functional inference.” Briefings in Bioinformatics, vol. 20, no. 4, Oxford University Press (OUP), July 2019, pp. 1568–77. Crossref, doi:10.1093/bib/bbx088.
Cao H, Ma Q, Chen X, Xu Y. DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings in Bioinformatics. Oxford University Press (OUP); 2019 Jul 19;20(4):1568–1577.
Journal cover image

Published In

Briefings in Bioinformatics

DOI

EISSN

1477-4054

ISSN

1467-5463

Publication Date

July 19, 2019

Volume

20

Issue

4

Start / End Page

1568 / 1577

Publisher

Oxford University Press (OUP)

Related Subject Headings

  • Bioinformatics
  • 0899 Other Information and Computing Sciences
  • 0802 Computation Theory and Mathematics
  • 0601 Biochemistry and Cell Biology