Literature DB >> 15499578

Recent developments in computational approaches for uncovering genomic homology.

Cedric Simillion1, Klaas Vandepoele, Yves Van de Peer.   

Abstract

Identifying genomic homology within and between genomes is essential when studying genome evolution. In the past years, different computational techniques have been developed to detect homology even when the actual similarity between homologous segments is low. Depending on the strategy used, these methods search for pairs of chromosomal segments between which either both gene content and order are conserved or gene content only. However, due to fact that, after their divergence, homologous segments can lose a different set of genes, these methods still often fail to detect genomic homology. Recently, more advanced approaches have been developed that can combine gene order and content information of multiple genomic segments.

Mesh:

Year:  2004        PMID: 15499578     DOI: 10.1002/bies.20127

Source DB:  PubMed          Journal:  Bioessays        ISSN: 0265-9247            Impact factor:   4.345


  8 in total

1.  PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Authors:  Sebastian Proost; Michiel Van Bel; Lieven Sterck; Kenny Billiau; Thomas Van Parys; Yves Van de Peer; Klaas Vandepoele
Journal:  Plant Cell       Date:  2009-12-29       Impact factor: 11.277

2.  Minimal absent words in prokaryotic and eukaryotic genomes.

Authors:  Sara P Garcia; Armando J Pinho; João M O S Rodrigues; Carlos A C Bastos; Paulo J S G Ferreira
Journal:  PLoS One       Date:  2011-01-31       Impact factor: 3.240

3.  A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.

Authors:  Hong-Yu Ou; Ling-Ling Chen; James Lonnen; Roy R Chaudhuri; Ali Bin Thani; Rebecca Smith; Natalie J Garton; Jay Hinton; Mark Pallen; Michael R Barer; Kumar Rajakumar
Journal:  Nucleic Acids Res       Date:  2006-01-09       Impact factor: 16.971

4.  Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.

Authors:  Xiyin Wang; Xiaoli Shi; Zhe Li; Qihui Zhu; Lei Kong; Wen Tang; Song Ge; Jingchu Luo
Journal:  BMC Bioinformatics       Date:  2006-10-12       Impact factor: 3.169

5.  Xenolog classification.

Authors:  Charlotte A Darby; Maureen Stolzer; Patrick J Ropp; Daniel Barker; Dannie Durand
Journal:  Bioinformatics       Date:  2017-03-01       Impact factor: 6.937

6.  OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.

Authors:  Soheil Jahangiri-Tazehkand; Limsoon Wong; Changiz Eslahchi
Journal:  Genomics Proteomics Bioinformatics       Date:  2017-11-11       Impact factor: 7.691

7.  CHSMiner: a GUI tool to identify chromosomal homologous segments.

Authors:  Zhen Wang; Guohui Ding; Zhonghao Yu; Lei Liu; Yixue Li
Journal:  Algorithms Mol Biol       Date:  2009-01-15       Impact factor: 1.405

8.  Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions.

Authors:  Tomas A Larsson; Frida Olsson; Gorel Sundstrom; Lars-Gustav Lundin; Sydney Brenner; Byrappa Venkatesh; Dan Larhammar
Journal:  BMC Evol Biol       Date:  2008-06-25       Impact factor: 3.260

  8 in total

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