Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D452-D455; doi:10.1093/nar/gkj041
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2433K) Freely available
Right arrow Screen PDF (467K) Freely available
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
Citing Articles
Right arrowScopus Links
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Byrne, K. P.
Right arrow Articles by Wolfe, K. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Byrne, K. P.
Right arrow Articles by Wolfe, K. H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2006, Vol. 34, Database issue D452-D455
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

Kevin P. Byrne* and Kenneth H. Wolfe

Department of Genetics, Smurfit Institute, University of Dublin, Trinity College Dublin 2, Ireland

*To whom correspondence should be addressed. Tel: +353 1 608 1288; Fax: +353 1 679 8558; Email: kevin.byrne{at}tcd.ie

Received August 10, 2005. Revised October 3, 2005. Accepted October 3, 2005.

The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven hemiascomycete yeast species. Three of these genomes are polyploid, and hence contain intra-genomic syntenic regions, the correct assembly of which is a particular success of YGOB. Designed to accurately assemble, display and score gene order relationships, YGOB is both an interactive tool for browsing genomic data, and a software engine now being used for evolutionary analyses on a whole-genome scale. Underlying the online interface is the YGOB database, which consists of homology assignments across the species, extensively curated based on sequence similarity and novelly, an appraisal of genomic context (synteny) in multiple genomes. Currently the YGOB database incorporates genome data from Saccharomyces cerevisiae, Candida glabrata, Saccharomyces castellii, Ashbya gossypii, Kluyveromyces lactis, Kluyveromyces waltii and Saccharomyces kluyveri, but the system is scaleable to accommodate additional genomes. This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at http://wolfe.gen.tcd.ie/ygob.


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
 J. Biol. Chem.Home page
K. Wielemans, C. Jean, S. Vissers, and B. Andre
Amino Acid Signaling in Yeast: Post-genome Duplication Divergence of the Stp1 and Stp2 Transcription Factors
J. Biol. Chem., January 8, 2010; 285(2): 855 - 865.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
Z. Luo and H. J. J. van Vuuren
Functional analyses of PAU genes in Saccharomyces cerevisiae
Microbiology, December 1, 2009; 155(12): 4036 - 4049.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Conde e Silva, I. R. Goncalves, M. Lemaire, E. Lesuisse, J. M. Camadro, and P. L. Blaiseau
KlAft, the Kluyveromyces lactis Ortholog of Aft1 and Aft2, Mediates Activation of Iron-Responsive Transcription Through the PuCACCC Aft-Type Sequence
Genetics, September 1, 2009; 183(1): 93 - 106.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Biol. CellHome page
Y. Nakajima, R. G. Tyers, C. C.L. Wong, J. R. Yates III, D. G. Drubin, and G. Barnes
Nbl1p: A Borealin/Dasra/CSC-1-like Protein Essential for Aurora/Ipl1 Complex Function and Integrity in Saccharomyces cerevisiae
Mol. Biol. Cell, March 15, 2009; 20(6): 1772 - 1784.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. J. A. van Hoek and P. Hogeweg
The Role of Mutational Dynamics in Genome Shrinkage
Mol. Biol. Evol., November 1, 2007; 24(11): 2485 - 2494.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. J. Penkett, J. A. Morris, V. Wood, and J. Bahler
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W330 - W334.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Y. Galperin
The Molecular Biology Database Collection: 2006 update.
Nucleic Acids Res., January 1, 2006; 34(Database issue): D3 - D5.
[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.