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Literature DB >> 22820205

ANGES: reconstructing ANcestral GEnomeS maps.

Bradley R Jones¹, Ashok Rajaraman, Eric Tannier, Cedric Chauve.

Abstract

SUMMARY: ANGES is a suite of Python programs that allows reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES can reconstruct ancestral genome maps for multichromosomal linear genomes and unichromosomal circular genomes. It implements methods inspired from techniques developed to compute physical maps of extant genomes. Examples of cereal, amniote, yeast or bacteria ancestral genomes are provided, computed with ANGES. AVAILABILITY: ANGES is freely available for download at http://paleogenomics.irmacs.sfu.ca/ANGES/. Documentation and examples are available together with the package. CONTACT: cedric.chauve@sfu.ca.

Entities: Species

Mesh：

Year: 2012 PMID： 22820205 DOI： 10.1093/bioinformatics/bts457

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

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Cited

24 in total

1. Reconstruction and evolutionary history of eutherian chromosomes.

Authors: Jaebum Kim; Marta Farré; Loretta Auvil; Boris Capitanu; Denis M Larkin; Jian Ma; Harris A Lewin
Journal: Proc Natl Acad Sci U S A Date: 2017-06-19 Impact factor: 11.205

2. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

Authors: Michael R Kanost; Estela L Arrese; Xiaolong Cao; Yun-Ru Chen; Sanjay Chellapilla; Marian R Goldsmith; Ewald Grosse-Wilde; David G Heckel; Nicolae Herndon; Haobo Jiang; Alexie Papanicolaou; Jiaxin Qu; Jose L Soulages; Heiko Vogel; James Walters; Robert M Waterhouse; Seung-Joon Ahn; Francisca C Almeida; Chunju An; Peshtewani Aqrawi; Anne Bretschneider; William B Bryant; Sascha Bucks; Hsu Chao; Germain Chevignon; Jayne M Christen; David F Clarke; Neal T Dittmer; Laura C F Ferguson; Spyridoula Garavelou; Karl H J Gordon; Ramesh T Gunaratna; Yi Han; Frank Hauser; Yan He; Hanna Heidel-Fischer; Ariana Hirsh; Yingxia Hu; Hongbo Jiang; Divya Kalra; Christian Klinner; Christopher König; Christie Kovar; Ashley R Kroll; Suyog S Kuwar; Sandy L Lee; Rüdiger Lehman; Kai Li; Zhaofei Li; Hanquan Liang; Shanna Lovelace; Zhiqiang Lu; Jennifer H Mansfield; Kyle J McCulloch; Tittu Mathew; Brian Morton; Donna M Muzny; David Neunemann; Fiona Ongeri; Yannick Pauchet; Ling-Ling Pu; Ioannis Pyrousis; Xiang-Jun Rao; Amanda Redding; Charles Roesel; Alejandro Sanchez-Gracia; Sarah Schaack; Aditi Shukla; Guillaume Tetreau; Yang Wang; Guang-Hua Xiong; Walther Traut; Tom K Walsh; Kim C Worley; Di Wu; Wenbi Wu; Yuan-Qing Wu; Xiufeng Zhang; Zhen Zou; Hannah Zucker; Adriana D Briscoe; Thorsten Burmester; Rollie J Clem; René Feyereisen; Cornelis J P Grimmelikhuijzen; Stavros J Hamodrakas; Bill S Hansson; Elisabeth Huguet; Lars S Jermiin; Que Lan; Herman K Lehman; Marce Lorenzen; Hans Merzendorfer; Ioannis Michalopoulos; David B Morton; Subbaratnam Muthukrishnan; John G Oakeshott; Will Palmer; Yoonseong Park; A Lorena Passarelli; Julio Rozas; Lawrence M Schwartz; Wendy Smith; Agnes Southgate; Andreas Vilcinskas; Richard Vogt; Ping Wang; John Werren; Xiao-Qiang Yu; Jing-Jiang Zhou; Susan J Brown; Steven E Scherer; Stephen Richards; Gary W Blissard
Journal: Insect Biochem Mol Biol Date: 2016-08-12 Impact factor: 4.714

3. Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan.

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Journal: Nat Genet Date: 2021-04-19 Impact factor: 38.330

4. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.

Authors: Florent Murat; Rongzhi Zhang; Sébastien Guizard; Raphael Flores; Alix Armero; Caroline Pont; Delphine Steinbach; Hadi Quesneville; Richard Cooke; Jerome Salse
Journal: Genome Biol Evol Date: 2014-01 Impact factor: 3.416

ANGES: reconstructing ANcestral GEnomeS maps.

1. Reconstruction and evolutionary history of eutherian chromosomes.

2. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

3. Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan.

4. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.

5. ProCARs: Progressive Reconstruction of Ancestral Gene Orders.

6. Ancestral Reconstruction.

7. Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

8. Linearization of ancestral multichromosomal genomes.

9. Models and algorithms for genome rearrangement with positional constraints.

10. Reconstruction of ancestral gene orders using intermediate genomes.