CAGE: Combinatorial Analysis of Gene-cluster Evolution

Overview

Journal J Comput Biol

Specialties Biology
Molecular Biology

Date 2010 Sep 30

PMID 20874406

Citations 4

Authors

Giltae Song

Louxin Zhang

Tomas Vinar

Webb Miller

Affiliations

Soon will be listed here.

Abstract

Much important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to acquire new functions. Current computational methods to extract evolutionary information from sequence data for such clusters are suboptimal, in part because accurate sequence data are often lacking in these genomic regions, making existing methods difficult to apply. We describe a new method for reconstructing the recent evolutionary history of gene clusters, and evaluate its performance on both simulated data and actual human gene clusters.

Citing Articles

Fast computation of a string duplication history under no-breakpoint-reuse.

Brejova B, Kravec M, Landau G, Vinar T Philos Trans A Math Phys Eng Sci. 2014; 372(2016):20130133.

PMID: 24751867 PMC: 3996574. DOI: 10.1098/rsta.2013.0133.

Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

Walker M, King B, Paigen K PLoS One. 2012; 7(4):e35274.

PMID: 22563380 PMC: 3338513. DOI: 10.1371/journal.pone.0035274.

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.

Song G, Riemer C, Dickins B, Kim H, Zhang L, Zhang Y Genome Biol Evol. 2012; 4(4):586-601.

PMID: 22454131 PMC: 3342878. DOI: 10.1093/gbe/evs032.

Conversion events in gene clusters.

Song G, Hsu C, Riemer C, Zhang Y, Kim H, Hoffmann F BMC Evol Biol. 2011; 11:226.

PMID: 21798034 PMC: 3161012. DOI: 10.1186/1471-2148-11-226.

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