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Toward community standards in the quest for orthologs

C. Dessimoz, T. Gabaldon, D. S. Roos, E. L. L. Sonnhammer, J. Herrero, A. Altenhoff, R. Apweiler, M. Ashburner, J. Blake, B. Boeckmann, A. Bridge, E. Bruford (+43 others)
2012 Bioinformatics  
The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact:  ...  The second 'Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges.  ...  We also thank the EBI, and Alison Barker in particular, for the organizational support.  ... 
doi:10.1093/bioinformatics/bts050 pmid:22332236 pmcid:PMC3307119 fatcat:j2jsdsoxrjfubbqp3euqzl4ppi

Toward community standards in the quest for orthologs

C Dessimoz, T Gabaldon, D S Roos, E L L Sonnhammer, J Herrero, A Altenhoff, R Apweiler, M Ashburner, J Blake, B Boeckmann, A Bridge, E Bruford (+19 others)
2012
The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications  ...  The second 'Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges.  ...  The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications.  ... 
doi:10.5167/uzh-155199 fatcat:5ofp23gvhvacxcw4ytbj6foxwu

The Quest for Orthologs benchmark service and consensus calls in 2020

Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, Josep Ll Gelpi (+11 others)
2020 Nucleic Acids Research  
To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org).  ...  The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution  ...  Since 2011, the Quest for Orthologs (QfO) makes available a Reference Proteomes dataset, providing a representative protein for each gene in the genome of selected species.  ... 
doi:10.1093/nar/gkaa308 pmid:32374845 pmcid:PMC7319555 fatcat:fuzbeoshlvegddgzcylkiwvqpu

Joining forces in the quest for orthologs

Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis
2009 Genome Biology  
Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts.  ...  and making sure we ran on time, to all participants in the meeting for their valuable ideas, and to Michael Ashburner from whom the idea for this valuable workshop also originated.  ...  Acknowledgements We are grateful to the European Science Foundation and the Wellcome Trust for their generous support, which made this meeting possible, to Pam Garland for coordinating our many requests  ... 
doi:10.1186/gb-2009-10-9-403 pmid:19785718 pmcid:PMC2768974 fatcat:5nyri4hzdvfhdhunsh342v3ihm

Advances and Applications in the Quest for Orthologs

2019 Molecular biology and evolution  
Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium.  ...  The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward  ...  Members of the Quest for Orthologs Consortium: Adrian Altenhoff, Judith A.  ... 
doi:10.1093/molbev/msz150 pmid:31241141 pmcid:PMC6759064 fatcat:ahhm3ev72nghlfyb5kfbjahnsu

Towards the Semantic Standardization of Orthology Content

Jesualdo Tomás Fernández-Breis, María Del Carmen Legaz-García, Hirokazu Chiba, Ikuo Uchiyama
2015 Workshop on Semantic Web Applications and Tools for Life Sciences  
In recent years OrthoXML permitted to advance in the standardization of the content for exchange within the orthology community, but the interest in exchanging content with other communities suggested  ...  In this work, we describe the advances done with the objective of the semantic standardization of orthology content.  ...  We would like to thank the organizers of the BioHackathon meeting (http://www.biohackathon.org) for providing us an invaluable opportunity to accomplish this work.  ... 
dblp:conf/swat4ls/Fernandez-Breis15 fatcat:7bydks273ndsll3uupfyefnmqe

Ten years of collaborative progress in the Quest for Orthologs

Benjamin Linard, Ingo Ebersberger, Shawn E McGlynn, Natasha Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, Paul D Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz (+3 others)
2021 Molecular biology and evolution  
Since 2009, this task has been the focus of the Quest for Orthologs (QFO) consortium.  ...  The 6th QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference.  ...  Acknowledgments We thank the National Institute for Basic Biology, the Japanese Society for Bioinformatics and the Daiko Foundation for supporting the 67th NIBB Conference/The 6th Quest for Orthologs Meeting  ... 
doi:10.1093/molbev/msab098 pmid:33822172 pmcid:PMC8321534 fatcat:vwgowuvdbjd3rgol2vksjshqse

The Orthology Ontology: development and applications

Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, María del Carmen Legaz-García, Ikuo Uchiyama
2016 Journal of Biomedical Semantics  
Conclusions: The Orthology Ontology can serve as a framework for the semantic standardization of orthology content and it will contribute to a better exploitation of orthology resources in biomedical research  ...  This shareable ontology enables the possibility to develop Linked Orthology Datasets and a meta-predictor of orthology through standardization for the representation of orthology databases.  ...  Availability The Orthology Ontology is freely available in OWL format to all users at http:// purl.org/net/orth and it is also provided by BioPortal and AberOWL at http:// bioportal.bioontology.org/ontologies  ... 
doi:10.1186/s13326-016-0077-x pmid:27259657 pmcid:PMC4893294 fatcat:qhjzekfuw5d7xpil32ncyhcvva

Roundup 2.0: enabling comparative genomics for over 1800 genomes

T. F. DeLuca, J. Cui, J.-Y. Jung, K. C. St. Gabriel, D. P. Wall
2012 Bioinformatics  
Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard.  ...  Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes.  ...  ACKNOWLEDGEMENTS Computations were run on the Orchestra cluster supported by the Harvard Medical School Research Information Technology Group.  ... 
doi:10.1093/bioinformatics/bts006 pmid:22247275 pmcid:PMC3289913 fatcat:ck54u2nvrfdyznxx2yiwghdm6i

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

Erik L.L. Sonnhammer, Gabriel Östlund
2014 Nucleic Acids Research  
InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273  ...  Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%.  ...  ACKNOWLEDGEMENTS This project was supported by BILS (Bioinformatics Infrastructure for Life Sciences).  ... 
doi:10.1093/nar/gku1203 pmid:25429972 pmcid:PMC4383983 fatcat:4jktqdmnqffjpnionzmmrps4iq

HieranoiDB: a database of orthologs inferred by Hieranoid

Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer
2016 Nucleic Acids Research  
In this first version, orthologs are available for the 66 Quest for Orthologs reference proteomes.  ...  It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root.  ...  . uk/reference proteomes) that make up the 2011 04 Quest for Orthologs (QfO) reference proteomes (17) .  ... 
doi:10.1093/nar/gkw923 pmid:27742821 pmcid:PMC5210627 fatcat:oj23tismqvgipciiu2fp23znkm

OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte
2018 Nucleic Acids Research  
OrthoInspector is one of the leading software suites for orthology relations inference.  ...  life, making OrthoInspector the most exhaustive orthology resource to date in terms of covered species (excluding viruses).  ...  ACKNOWLEDGEMENTS We thank the Bio-statistics, Informatics and Complex System platform (BICS) and BISTRO bioinformatics platforms for informatics support and the European Grid Infrastructure for cloud computing  ... 
doi:10.1093/nar/gky1068 pmid:30380106 pmcid:PMC6323921 fatcat:dhx4n4gcxffrhf3fgcyf4geinm

Progress in quickly finding orthologs as reciprocal best hits [article]

Julie Eliene Hernandez-Salmeron, Gabriel Moreno-Hagelsieb
2020 bioRxiv   pre-print
not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH).  ...  The program producing the most similar number of RBH as blastp was MMseqs2. This program was also resulted in the lowest error estimates compared to any of the programs used.  ...  Acknowledgements This work was supported by a Discovery Grant to GM-H from The Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1101/2020.05.04.077222 fatcat:rsdcuxfgffc55ppxitqxwwpw4e

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Brigitte Boeckmann, Marina Marcet-Houben, Jonathan A. Rees, Kristoffer Forslund, Jaime Huerta-Cepas, Matthieu Muffato, Pelin Yilmaz, Ioannis Xenarios, Peer Bork, Suzanna E. Lewis, Toni Gabaldón
2015 Genome Biology and Evolution  
Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions.  ...  are incongruent in at least one of the species trees.  ...  Acknowledgments The authors wish to thank Vivienne Baillie Gerritsen for proofreading. This work was supported by the Swiss Federal  ... 
doi:10.1093/gbe/evv121 pmid:26133389 pmcid:PMC4524488 fatcat:sjy44b6ss5dkjfc7ccjtoy42ri

Towards Consensus Gene Ages

Benjamin J. Liebeskind, Claire D. McWhite, Edward M. Marcotte
2016 Genome Biology and Evolution  
We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis.  ...  However, most studies use only a point estimate of a gene's age, neglecting the substantial uncertainty involved in this estimation.  ...  Acknowledgments The authors would especially like to acknowledge the Quest for Orthologs consortium and those who contributed their algorithms to the benchmarking tool for making their data  ... 
doi:10.1093/gbe/evw113 pmid:27259914 pmcid:PMC4943184 fatcat:6hmvs56kyfbnfkkjjoum6w7ogy
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