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COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations

Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka
2006 Computer applications in the biosciences : CABIOS  
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

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
2008 Trends in Genetics  
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]

Adrian M. Altenhoff, Christophe Dessimoz
2012 Msphere  
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

Fredj Tekaia
2016 Genomics Insights  
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]

Adrian M. Altenhoff, Natasha M. Glover, Christophe Dessimoz
2019 Msphere  
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

E. V. Kriventseva, N. Rahman, O. Espinosa, E. M. Zdobnov
2007 Nucleic Acids Research  
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

D. M. Kristensen, Y. I. Wolf, A. R. Mushegian, E. V. Koonin
2011 Briefings in Bioinformatics  
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?

Toni Gabaldón
2008 Genome Biology  
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

Bruno T. L. Nichio, Jeroniza Nunes Marchaukoski, Roberto Tadeu Raittz
2017 Frontiers in Genetics  
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]

Fatemeh Ashari Ghomi, University Of Canterbury
2018
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

Ester Alvarenga, Santos Buiate
unpublished
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