Literature DB >> 12798040

Gene teams: a new formalization of gene clusters for comparative genomics.

Nicolas Luc1, Jean-Loup Risler, Anne Bergeron, Mathieu Raffinot.   

Abstract

This paper describes an efficient algorithm based on a new concept called gene team for detecting conserved gene clusters among an arbitrary number of chromosomes. Within the clusters, neither the order of the genes nor their orientation need be conserved. In addition, insertion of foreign genes within the clusters are permitted to a user-defined extent. This algorithm has been implemented in a publicly available TEAM software that proves to be an efficient tool for systematic searches of conserved gene clusters. Examples of actual biological results are provided. The software is downloadable from http://www-igm.univ-mlv.fr/ approximately raffinot/geneteam.html.

Mesh：

Year:  2003        PMID： 12798040     DOI： 10.1016/s1476-9271(02)00097-x

Source DB:  PubMed          Journal:  Comput Biol Chem        ISSN： 1476-9271            Impact factor:   2.877


  19 in total

1.  Identification of genomic features using microsyntenies of domains: domain teams.

Authors:  Sophie Pasek; Anne Bergeron; Jean-Loup Risler; Alexandra Louis; Emmanuelle Ollivier; Mathieu Raffinot
Journal:  Genome Res       Date:  2005-05-17       Impact factor: 9.043

2.  Large-scale analysis of gene clustering in bacteria.

Authors:  Qingwu Yang; Sing-Hoi Sze
Journal:  Genome Res       Date:  2008-04-04       Impact factor: 9.043

3.  A scenario of mitochondrial genome evolution in maize based on rearrangement events.

Authors:  Aude Darracq; Jean-Stéphane Varré; Pascal Touzet
Journal:  BMC Genomics       Date:  2010-04-09       Impact factor: 3.969

4.  CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.

Authors:  Christian Rödelsperger; Christoph Dieterich
Journal:  PLoS One       Date:  2010-01-28       Impact factor: 3.240

5.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Authors:  Yupeng Wang; Haibao Tang; Jeremy D Debarry; Xu Tan; Jingping Li; Xiyin Wang; Tae-ho Lee; Huizhe Jin; Barry Marler; Hui Guo; Jessica C Kissinger; Andrew H Paterson
Journal:  Nucleic Acids Res       Date:  2012-01-04       Impact factor: 16.971

6.  CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data.

Authors:  Tania Dottorini; Pietro Palladino; Nicola Senin; Tania Persampieri; Roberta Spaccapelo; Andrea Crisanti
Journal:  PLoS One       Date:  2013-06-18       Impact factor: 3.240

7.  Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster.

Authors:  Ismael A Vergara; Nansheng Chen
Journal:  BMC Genomics       Date:  2010-09-24       Impact factor: 3.969

8.  Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus.

Authors:  Fabienne Ripoll; Sophie Pasek; Chantal Schenowitz; Carole Dossat; Valérie Barbe; Martin Rottman; Edouard Macheras; Beate Heym; Jean-Louis Herrmann; Mamadou Daffé; Roland Brosch; Jean-Loup Risler; Jean-Louis Gaillard
Journal:  PLoS One       Date:  2009-06-19       Impact factor: 3.240

9.  Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

Authors:  Ikuo Uchiyama
Journal:  BMC Genomics       Date:  2008-10-31       Impact factor: 3.969

10.  Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice.

Authors:  Yupeng Wang
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416
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