Skip Navigation



Nucleic Acids Research Advance Access published online on November 27, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl857
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (161K) Freely available
Right arrow Screen PDF (164K) Freely available
Right arrowOA All Versions of this Article:
35/suppl_1/D127    most recent
gkl857v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Pachkov, M.
Right arrow Articles by van Nimwegen, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pachkov, M.
Right arrow Articles by van Nimwegen, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SwissRegulon: a database of genome-wide annotations of regulatory sites

Mikhail Pachkov1,2, Ionas Erb1,2, Nacho Molina1,2 and Erik van Nimwegen1,2,*

1 Biozentrum, The University of Basel Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland 2 Swiss Institute of Bioinformatics Switzerland

*To whom correspondence should be addressed. Tel: +41 61 267 1576; Fax: +41 61 267 1584; Email: erik.vannimwegen{at}unibas.ch

Received August 14, 2006. Revised September 17, 2006. Accepted October 1, 2006.

SwissRegulon (http://www.swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes in combination with, whenever available, known sites from the literature, and ChIP-on-chip binding data. Currently SwissRegulon contains annotations for yeast and 17 prokaryotic genomes. The database provides information about the sequence, location, orientation, posterior probability and, whenever available, binding factor of each annotated site. To enable easy viewing of the regulatory site annotations in the context of other features annotated on the genomes, the sites are displayed using the GBrowse genome browser interface and can be queried based on any annotated genomic feature. The database can also be queried for regulons, i.e. sites bound by a common factor.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
Y.-W. Chang, F.-G. Robert Liu, N. Yu, H.-M. Sung, P. Yang, D. Wang, C.-J. Huang, M.-C. Shih, and W.-H. Li
Roles of cis- and trans-Changes in the Regulatory Evolution of Genes in the Gluconeogenic Pathway in Yeast
Mol. Biol. Evol., September 1, 2008; 25(9): 1863 - 1875.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. Mustonen, J. Kinney, C. G. Callan Jr, and M. Lassig
Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites
PNAS, August 26, 2008; 105(34): 12376 - 12381.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Klein, S. Leupold, R. Munch, C. Pommerenke, T. Johl, U. Karst, L. Jansch, D. Jahn, and I. Retter
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W460 - W464.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
H. Schober, V. Kalck, M. A. Vega-Palas, G. Van Houwe, D. Sage, M. Unser, M. R. Gartenberg, and S. M. Gasser
Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast
Genome Res., February 1, 2008; 18(2): 261 - 271.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. J. Leach, Z. Zhang, C. Lu, M. J. Kearsey, and Z. Luo
The Role of Cis-Regulatory Motifs and Genetical Control of Expression in the Divergence of Yeast Duplicate Genes
Mol. Biol. Evol., November 1, 2007; 24(11): 2556 - 2565.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-K. Tsai, M.-Y. Chou, C.-H. Shih, G. T.-W. Huang, T.-H. Chang, and W.-H. Li
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W221 - W226.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.