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PMID: 12140322 Published · ppublish English Evaluation Study Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

GenomeHistory: a software tool and its application to fully sequenced genomes.

Nucleic acids research ·Vol. 30 ·No. 15 ·2002-08-01 ·Pages 3378-86

Conant GC, Wagner A

Abstract

We present a publicly available software tool (http://www.unm.edu/~compbio/software/GenomeHistory) that identifies all pairs of duplicate genes in a genome and then determines the degree of synonymous and non-synonymous divergence between each duplicate pair. Using this tool, we analyze the relations between (i) gene function and the propensity of a gene to duplicate and (ii) the number of genes in a gene family and the family's rate of sequence evolution. We do so for the complete genomes of four eukaryotes (fission and budding yeast, fruit fly and nematode) and one prokaryote (Escherichia coli). For some classes of genes we observe a strong relationship between gene function and a gene's propensity to undergo duplication. Most notably, ribosomal genes and transcription factors appear less likely to undergo gene duplication than other genes. In both fission and budding yeast, we see a strong positive correlation between the selective constraint on a gene and the size of the gene family of which this gene is a member. In contrast, a weakly negative such correlation is seen in multicellular eukaryotes.

MeSH Terms
Animals Caenorhabditis elegans/genetics Drosophila melanogaster/genetics Escherichia coli/genetics Evolution, Molecular Gene Duplication Genes, Duplicate/physiology Genome Genomics/methods Saccharomyces cerevisiae/genetics Schizosaccharomyces/genetics Sequence Analysis, DNA/methods Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Conant Gavin C
Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA. gconant@unm.edu
Wagner Andreas
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkf449
Email
gconant@unm.edu
Published
2002-08-01
Pages
3378-86
Language
English
Region
England
NLM ID
0411011
PMCID
PMC137074
Subset
IM
Grants
NIGMS NIH HHS · R01 GM063882 · United States
NIGMS NIH HHS · GM063882-01 · United States
External Links
PubMed source DOI: 10.1093/nar/gkf449 PMC Full Text View journal details
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