Skip Navigation



Bioinformatics Advance Access published online on July 9, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth397
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/18/3643    most recent
bth397v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Haas, B. J.
Right arrow Articles by Salzberg, S. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Haas, B. J.
Right arrow Articles by Salzberg, S. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received May 26, 2004
Accepted June 29, 2004

Applications note

DAGchainer: A tool for mining segmental genome duplications and synteny

Brian J. Haas 1*, Arthur L. Delcher 1, Jennifer R. Wortman 1, Steven L. Salzberg 1

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA

* To whom correspondence should be addressed. E-mail: bhaas{at}tigr.org.


  Abstract

Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG). These chains of collinear gene pairs can represent segmentally duplicated regions and genes within a single genome, or syntenic regions between related genomes. Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer.


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
 Brief BioinformHome page
J. Salse, M. Abrouk, F. Murat, U. M. Quraishi, and C. Feuillet
Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
Brief Bioinform, August 31, 2009; (2009) bbp037v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Hachiya, Y. Osana, K. Popendorf, and Y. Sakakibara
Accurate identification of orthologous segments among multiple genomes
Bioinformatics, April 1, 2009; 25(7): 853 - 860.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
H. Tang, X. Wang, J. E. Bowers, R. Ming, M. Alam, and A. H. Paterson
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
Genome Res., December 1, 2008; 18(12): 1944 - 1954.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Freeling, E. Lyons, B. Pedersen, M. Alam, R. Ming, and D. Lisch
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
Genome Res., December 1, 2008; 18(12): 1924 - 1937.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
E. Lyons, B. Pedersen, J. Kane, M. Alam, R. Ming, H. Tang, X. Wang, J. Bowers, A. Paterson, D. Lisch, et al.
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
Plant Physiology, December 1, 2008; 148(4): 1772 - 1781.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. A. Campbell, W. Zhu, N. Jiang, H. Lin, S. Ouyang, K. L. Childs, B. J. Haas, J. P. Hamilton, and C. R. Buell
Identification and Characterization of Lineage-Specific Genes within the Poaceae
Plant Physiology, December 1, 2007; 145(4): 1311 - 1322.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Ouyang, W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R. L. Malek, Y. Lee, L. Zheng, et al.
The TIGR Rice Genome Annotation Resource: improvements and new features
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D883 - D887.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
C. Soderlund, W. Nelson, A. Shoemaker, and A. Paterson
SyMAP: A system for discovering and viewing syntenic regions of FPC maps.
Genome Res., September 1, 2006; 16(9): 1159 - 1168.
[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.