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COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
2006
Computer applications in the biosciences : CABIOS
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Results: We propose a new method, COCO-CL, for hierarchical clustering of homology relations and identification of orthologous groups of genes. ...
Unlike previous approaches, which are based on pairwise sequence comparisons, our method explores the correlation of evolutionary histories of individual genes in a more global context. ...
Funding to pay the Open Access publication charges was provided by the intramural research program of the National Institutes of Health. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btl009
pmid:16434444
pmcid:PMC1620014
fatcat:qndlgpbim5de5dahdavqscea7u
The quest for orthologs: finding the corresponding gene across genomes
2008
Trends in Genetics
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Tree-based methods
Correlation Coefficient-based Clustering (COCO-CL) The COCO-CL program takes the non-transitivity of phylogenetic relations within a set of homologous proteins into account using a ...
Pros: COCO-CL infers orthologs and paralogs from pre-computed homologs in a hierarchical framework without a species tree. The COCO-CL program and refined COG dataset are freely available. ...
doi:10.1016/j.tig.2008.08.009
pmid:18819722
fatcat:4w6qrixl7naw7aoqko73vruavq
Inferring Orthology and Paralogy
[chapter]
2012
Msphere
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We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. ...
Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments. ...
Acknowledgments We thank Stefan Zoller for helpful feedback on the manuscript. ...
doi:10.1007/978-1-61779-582-4_9
pmid:22407712
fatcat:52mxshbwvzffrllmaipbidh5ky
Inferring Orthologs: Open Questions and Perspectives
2016
Genomics Insights
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Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate ...
With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. ...
Acknowledgments I thank Bernard Dujon for constant support, Pedro Alzari for his careful reading of the manuscript and his suggestions, and Thomas Rolland for constructive discussions. ...
doi:10.4137/gei.s37925
pmid:26966373
pmcid:PMC4778853
fatcat:eo36owlqzvcnhjvsfwwwzicxei
Inferring Orthology and Paralogy
[chapter]
2019
Msphere
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We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. ...
Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments. ...
Acknowledgments We thank Stefan Zoller for helpful feedback on an earlier version of the manuscript. ...
doi:10.1007/978-1-4939-9074-0_5
pmid:31278664
fatcat:bfegalnlurdm3kivngq2dbhhdq
OrthoDB: the hierarchical catalog of eukaryotic orthologs
2007
Nucleic Acids Research
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Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained ...
We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects ...
Conflict of interest statement. None declared. ...
doi:10.1093/nar/gkm845
pmid:17947323
pmcid:PMC2238902
fatcat:iwwdxbt3evcs5f73frxd6z4jbu
Computational methods for Gene Orthology inference
2011
Briefings in Bioinformatics
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The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree. ...
Once the two trees are accurately constructed, orthologs are straightforwardly identified by the definition of orthology as those homologs that are related by speciation, rather than gene duplication, ...
COrrelation COefficient-based Clustering (COCO-CL) Uses a measure of sequence distance between evolutionary histories of homologous genes instead of a species tree to construct a hierarchy of clusters. ...
doi:10.1093/bib/bbr030
pmid:21690100
pmcid:PMC3178053
fatcat:hbxflsbzc5gnrf7svljpuek7su
Large-scale assignment of orthology: back to phylogenetics?
2008
Genome Biology
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Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. ...
L La ar rg ge e--s sc ca al le e a as ss si ig gn nm me en nt t o of f o or rt th ho ol lo og gy y: : b ba ac ck k t to o p ph hy yl lo og ge en ne et ti ic cs s? ? ...
For instance, COCO-CL subdivides a given orthologous group on the basis of the correlation coefficient between their sequences, as inferred from a multiple sequence alignment [19] . ...
doi:10.1186/gb-2008-9-10-235
pmid:18983710
pmcid:PMC2760865
fatcat:q7zeme67nfgdtftn5gomn6pomy
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives
2017
Frontiers in Genetics
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most promising ones in the prediction of orthologous groups. ...
Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. ...
Clustering (COCO-CL), COCO-CL (Raja et al., 2006) ; of Automatic Clustering of Orthologs and In-paralogs (InParanoid) (O'Brien, 2004) leading to the appearance of various tools such as the a Markov ...
doi:10.3389/fgene.2017.00165
pmid:29163633
pmcid:PMC5674930
fatcat:kl53wnq3unaxpoytoutf66olry
A study of protein coding genes in Enterobacteriaceae family: essentiality of genes and orthology
[article]
2018
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We introduce an ortholog clustering algorithm that can be used to nd orthologous genes to help with annotating genomes, as well as nding the evolutionary relationships between them. ...
We then compare the accuracy of this tool with other well-known models and discuss ways for improving the accuracy of the method. ...
COCO-CL [Jothi et al., 2006] has used a similar idea in which it uses hierarchical clustering for defining orthologs within a cluster of homologous genes. ...
doi:10.26021/7562
fatcat:hbqvdo2kwvbwphum3t37xfwkzm
UKnowledge ESTABLISHMENT OF BIOTROPHY BY THE MAIZE ANTHRACNOSE PATHOGEN COLLETOTRICHUM GRAMINICOLA: USE OF BIOINFORMATICS AND TRANSCRIPTOMICS TO ADDRESS THE POTENTIAL ROLES OF SECRETION, STRESS RESPONSE, AND SECRETED PROTEINS
unpublished
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In the first approach I used results generated by the programs Ortho-MCL and Coco-CL (C-CL) (COrrelation COefficient-based CLustering) (Jothi et al., 2006; Li et al., 2003) . ...
C-CL is a hierarchical clustering method that does not rely on pairwise sequence comparisons as OrthoMCL does, but utilizes a more global approach that can 'refine' the results so that distant paralogs ...
fatcat:6756i4wqyrd5zfeecsc72tjm2a