Literature DB >> 15247098

DAGchainer: a tool for mining segmental genome duplications and synteny.

Brian J Haas1, Arthur L Delcher, Jennifer R Wortman, Steven L Salzberg.   

Abstract

SUMMARY: 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.

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Year:  2004        PMID： 15247098     DOI： 10.1093/bioinformatics/bth397

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  162 in total

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Journal:  Bioinformatics       Date:  2012-04-11       Impact factor: 6.937

2.  SyMAP: A system for discovering and viewing syntenic regions of FPC maps.

Authors:  Carol Soderlund; William Nelson; Austin Shoemaker; Andrew Paterson
Journal:  Genome Res       Date:  2006-09       Impact factor: 9.043

3.  Many or most genes in Arabidopsis transposed after the origin of the order Brassicales.

Authors:  Michael Freeling; Eric Lyons; Brent Pedersen; Maqsudul Alam; Ray Ming; Damon Lisch
Journal:  Genome Res       Date:  2008-10-03       Impact factor: 9.043

4.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps.

Authors:  Haibao Tang; Xiyin Wang; John E Bowers; Ray Ming; Maqsudul Alam; Andrew H Paterson
Journal:  Genome Res       Date:  2008-10-02       Impact factor: 9.043

5.  The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut.

Authors:  David John Bertioli; Steven B Cannon; Lutz Froenicke; Guodong Huang; Andrew D Farmer; Ethalinda K S Cannon; Xin Liu; Dongying Gao; Josh Clevenger; Sudhansu Dash; Longhui Ren; Márcio C Moretzsohn; Kenta Shirasawa; Wei Huang; Bruna Vidigal; Brian Abernathy; Ye Chu; Chad E Niederhuth; Pooja Umale; Ana Cláudia G Araújo; Alexander Kozik; Kyung Do Kim; Mark D Burow; Rajeev K Varshney; Xingjun Wang; Xinyou Zhang; Noelle Barkley; Patrícia M Guimarães; Sachiko Isobe; Baozhu Guo; Boshou Liao; H Thomas Stalker; Robert J Schmitz; Brian E Scheffler; Soraya C M Leal-Bertioli; Xu Xun; Scott A Jackson; Richard Michelmore; Peggy Ozias-Akins
Journal:  Nat Genet       Date:  2016-02-22       Impact factor: 38.330

Review 6.  Visualizing genomes: techniques and challenges.

Authors:  Cydney B Nielsen; Michael Cantor; Inna Dubchak; David Gordon; Ting Wang
Journal:  Nat Methods       Date:  2010-02-25       Impact factor: 28.547

7.  Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.

Authors:  Joelle Amselem; Christina A Cuomo; Jan A L van Kan; Muriel Viaud; Ernesto P Benito; Arnaud Couloux; Pedro M Coutinho; Ronald P de Vries; Paul S Dyer; Sabine Fillinger; Elisabeth Fournier; Lilian Gout; Matthias Hahn; Linda Kohn; Nicolas Lapalu; Kim M Plummer; Jean-Marc Pradier; Emmanuel Quévillon; Amir Sharon; Adeline Simon; Arjen ten Have; Bettina Tudzynski; Paul Tudzynski; Patrick Wincker; Marion Andrew; Véronique Anthouard; Ross E Beever; Rolland Beffa; Isabelle Benoit; Ourdia Bouzid; Baptiste Brault; Zehua Chen; Mathias Choquer; Jérome Collémare; Pascale Cotton; Etienne G Danchin; Corinne Da Silva; Angélique Gautier; Corinne Giraud; Tatiana Giraud; Celedonio Gonzalez; Sandrine Grossetete; Ulrich Güldener; Bernard Henrissat; Barbara J Howlett; Chinnappa Kodira; Matthias Kretschmer; Anne Lappartient; Michaela Leroch; Caroline Levis; Evan Mauceli; Cécile Neuvéglise; Birgitt Oeser; Matthew Pearson; Julie Poulain; Nathalie Poussereau; Hadi Quesneville; Christine Rascle; Julia Schumacher; Béatrice Ségurens; Adrienne Sexton; Evelyn Silva; Catherine Sirven; Darren M Soanes; Nicholas J Talbot; Matt Templeton; Chandri Yandava; Oded Yarden; Qiandong Zeng; Jeffrey A Rollins; Marc-Henri Lebrun; Marty Dickman
Journal:  PLoS Genet       Date:  2011-08-18       Impact factor: 5.917

8.  Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids.

Authors:  Eric Lyons; Brent Pedersen; Josh Kane; Maqsudul Alam; Ray Ming; Haibao Tang; Xiyin Wang; John Bowers; Andrew Paterson; Damon Lisch; Michael Freeling
Journal:  Plant Physiol       Date:  2008-10-24       Impact factor: 8.340

9.  The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Authors:  Ignazio Verde; Albert G Abbott; Simone Scalabrin; Sook Jung; Shengqiang Shu; Fabio Marroni; Tatyana Zhebentyayeva; Maria Teresa Dettori; Jane Grimwood; Federica Cattonaro; Andrea Zuccolo; Laura Rossini; Jerry Jenkins; Elisa Vendramin; Lee A Meisel; Veronique Decroocq; Bryon Sosinski; Simon Prochnik; Therese Mitros; Alberto Policriti; Guido Cipriani; Luca Dondini; Stephen Ficklin; David M Goodstein; Pengfei Xuan; Cristian Del Fabbro; Valeria Aramini; Dario Copetti; Susana Gonzalez; David S Horner; Rachele Falchi; Susan Lucas; Erica Mica; Jonathan Maldonado; Barbara Lazzari; Douglas Bielenberg; Raul Pirona; Mara Miculan; Abdelali Barakat; Raffaele Testolin; Alessandra Stella; Stefano Tartarini; Pietro Tonutti; Pere Arús; Ariel Orellana; Christina Wells; Dorrie Main; Giannina Vizzotto; Herman Silva; Francesco Salamini; Jeremy Schmutz; Michele Morgante; Daniel S Rokhsar
Journal:  Nat Genet       Date:  2013-03-24       Impact factor: 38.330

10.  Identification and characterization of lineage-specific genes within the Poaceae.

Authors:  Matthew A Campbell; Wei Zhu; Ning Jiang; Haining Lin; Shu Ouyang; Kevin L Childs; Brian J Haas; John P Hamilton; C Robin Buell
Journal:  Plant Physiol       Date:  2007-10-19       Impact factor: 8.340
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