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Methods: SyMAP: A system for discovering and viewing syntenic regions of FPC maps
- Carol Soderlund,
- William Nelson,
- Austin Shoemaker,
- and Andrew Paterson
Genome Res. September 2006 16: 1159-1168; doi:10.1101/gr.5396706
...larger in maize than in rice. Since the BESs and markers in the FPC map do not cover the , there will be many possible anchors that cannot be detected. Therefore, there will be many genes in rice that do not appear to have a homologous sequence in maize. Moreover, the hybridized markers in FPC...
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Methods: Building Genomic Profiles for Uncovering Segmental Homology in the Twilight Zone
- Cedric Simillion,
- Klaas Vandepoele,
- Yvan Saeys,
- and Yves Van de Peer
Genome Res. June 2004 14: 1095-1106; doi:10.1101/gr.2179004
...of intragenomic and intergenomic homologous genes were determined using the method of Rost ( 1999 ). Consequently, i-ADHoRe was run on the Arabidopsis and rice data sets separately and on a combined Arabidopsis –rice data set. We used a gap size of 30, a quality factor of 0.9, and a probability cutoff of 0...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...functionalities. Results Identifying sister chromosome regions based on conserved gene order Paralogs derived from WGD are expected to be located in chromosome regions of shared ancestry. To help identify such regions, we first determined fish–human gene homology relationships by exhaustive, ‘‘all...
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Methods: Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
- Haibao Tang,
- Xiyin Wang,
- John E. Bowers,
- Ray Ming,
- Maqsudul Alam,
- and Andrew H. Paterson
Genome Res. December 2008 18: 1944-1954; Published in Advance October 2, 2008, doi:10.1101/gr.080978.108
...on information from only one species. New angiosperm sequences ( Table 1 ) promise to qualitatively improve our deductions about the evolution of angiosperm gene repertoire and arrangement. Arabidopsis ( Arabidopsis Genome Initiative 2000 ), rice ( Oryza sativa ) ( International Rice Genome Sequencing Project...
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LETTER: Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
- Corrinne E. Grover,
- HyeRan Kim,
- Rod A. Wing,
- Andrew H. Paterson,
- and Jonathan F. Wendel
Genome Res. August 2004 14: 1474-1482; Published in Advance July 15, 2004, doi:10.1101/gr.2673204
...the average Arabidopsis gene density of 1 gene per 4.5 kb of sequence ( The Arabidopsis Genome Initiative 2000 ) and similar to the average gene density in rice ( Rice Chromosome 10 Sequencing Consortium 2003 ). The CesA1 region appears to be part of a gene island, as the gene density is fairly high...
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ARTICLE: Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
- Nitin S. Baliga,
- Richard Bonneau,
- Marc T. Facciotti,
- Min Pan,
- Gustavo Glusman,
- Eric W. Deutsch,
- Paul Shannon,
- Yulun Chiu,
- Rueyhung Sting Weng,
- Rueichi Richie Gan,
- Pingliang Hung,
- Shailesh V. Date,
- Edward Marcotte,
- Leroy Hood,
- and Wailap Victor Ng
Genome Res. November 2004 14: 2221-2234; doi:10.1101/gr.2700304
...( Vandepoele et al. 2002 ) to study a higher-confidence subset of 1459 orthologous pairs to identify regions in the two large halophilic archaeal chromosomes with conserved gene order and orientation (for a description of the ADHoRe software, see Supplemental material). The regions of micro-colinearity...

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