DOOR2

  • Complete and reliable operon database covering 2072 bacteria genomes and with overall accuracy of ~90% evaluated by Brouwer (2008) on Brief Bioinformatics.
  • Massive alternative TUs (transcription units) from experiments and predicted by RNA-seq.
  • One-stop operon-centered resources including alternative transcrioption units, transcription factor binding motif, transcription terminator, gene exression by microarray and RNA-seq and conserve operons accross multiple bacteria genomes.
  • Intuitive JBrowse-based genome browser supporting exploring all data in an intutive visualization manner.
  • A google-like keyword based engine for easier search than ever, like NC_000913, lactose, b0001, lacZ, coli, MG1655.

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  • 7/22/2013, Xizeng presented DOOR 2 poster on DOE BESC Retreat 2013.
  • 2/6/2013, Xizeng and Chuan started to develop new web interface. Xin and Hanyuan are involved later.
  • 12/6/2013, Chuan, Xin and Qin started operon prediction and TU prediction.
  • 11/2012, Xizeng and Qin started to conceived the ideas of DOOR 2.0

The overall statistics of DOOR2

With operons* With Transcription Units(TUs)
#species2,072 #species24
#chromosomes2,205 #chromosomes24
#plasmids1,645 #plasmids0
#operons1,323,902 #TUs253,300
MOPC582.5 TPC10,554
MOPP24.0 TPP0
#single-gene operons2,578,949 --
SOPC1134.7 --
SOPP46.7 --

MOPC: multi-gene operons per chromosome

MOPP: multi-gene operons per plasmid

SOPC: single-gene operons per chromosome

SOPP: single-gene operons per plasmid

TPC: TUs per chromosome

TPP: TUs per plasmid

With cis-regulatory elements
#species203
#chromosomes224
#plasmids13
#TFs302
#TFBS6,489

TFs: transcription factors

TFBSs: transcription factor binding sites

With terminator*
#species2,072
#chromosomes2,205
#plasmids1,645
#terminators3,456,718

* ther terminators included in DOOR2 are all intrinsic terminators

Conserved Operons
#COP6,975,454
#COPPO5.3

COP: conserved operon pairs

COPPO: conserved operon pairs per operon

Please cite the following papers if you use our database:

  1. X. Mao*, Q. Ma*, C. Zhou, X. Chen, H. Zhang, J. Yang, F. Mao, W. Lai and Y Xu. DOOR 2.0: DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Being reviewed by NAR Special Database Issue, 2013.
  2. F. Mao, P. Dam, J. Chou, V. Olman, Y. Xu, DOOR: a Database of prOkaryotic OpeRons, Nucl. Acids Res. 37: D459-D463, 2009.
  3. P. Dam, V Olman, K. Harris, Z. Su, Ying Xu, Operon prediction using both genome-specific and general genome information, Nucleic Acids Research, 35:288 - 298, 2007.