ArticleNucleic acids research2005
Correlation between sequence conservation and the genomic context after gene duplication.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 54 citations in OpenAlex.
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- Primary orthologs from local sequence context.BMC bioinformatics · 2020Article
- Conserved Critical Evolutionary Gene Structures in Orthologs.Journal of molecular evolution · 2019Article
- Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.Scientific reports · 2016Article
- Homoeologs: What Are They and How Do We Infer Them?Trends in plant science · 2016Review
- Long-term asymmetrical acceleration of protein evolution after gene duplication.Genome biology and evolution · 2014Article
- To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs.BMC evolutionary biology · 2013Article
- Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat.Plant physiology · 2013Article
- The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae.Journal of virology · 2012Article
- A graph-theoretic approach for inparalog detection.BMC bioinformatics · 2012Article
- BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity.BMC systems biology · 2012Article
- Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates.BMC evolutionary biology · 2011Article
- Positional orthology: putting genomic evolutionary relationships into context.Briefings in bioinformatics · 2011Review
- Enrichment of homologs in insignificant BLAST hits by co-complex network alignment.BMC bioinformatics · 2010Article
- Gene socialization: gene order, GC content and gene silencing in Salmonella.BMC genomics · 2009Article
- PanCGH: a genotype-calling algorithm for pangenome CGH data.Bioinformatics (Oxford, England) · 2009Article
- PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.Nucleic acids research · 2009Article
- Phylogenetic and functional assessment of orthologs inference projects and methods.PLoS computational biology · 2009Article
- Algorithm of OMA for large-scale orthology inference.BMC bioinformatics · 2008Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two genomes (i.e. inparalogs). For these duplicated genes we investigate whether the gene that is most similar on the sequence level is also the gene that has retained the ancestral gene-neighborhood. Although the majority of investigated cases show a consistent pattern between sequence similarity and gene-neighborhood conservation, a substantial fraction, 29-38%, is inconsistent. The observation of inconsistency is not the result of a chance outcome owing to a lack of divergence time between inparalogs, but rather it seems to be the result of a chance outcome caused by very similar rates of sequence evolution of both inparalogs relative to their ortholog. If one-to-one orthologous relationships are required, it is advisable to combine contextual information (i.e. gene-neighborhood in prokaryotes and co-expression in eukaryotes) with protein sequence information to predict the most probable functional equivalent ortholog in the presence of inparalogs.
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