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Big data and other challenges in the quest for orthologs

E. L. L. Sonnhammer, T. Gabaldon, A. W. Sousa da Silva, M. Martin, M. Robinson-Rechavi, B. Boeckmann, P. D. Thomas, C. Dessimoz
2014 Bioinformatics  
Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting.  ...  However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale  ...  ACKNOWLEDGEMENTS Members of the Quest for Orthologs Consortium: Adrian Altenhoff, Judith Blake, Brigitte Boeckmann, Mike Cherry, Hirokazu Chiba, Vincent Daubin, Todd DeLuca, Christophe  ... 
doi:10.1093/bioinformatics/btu492 pmid:25064571 pmcid:PMC4201156 fatcat:llypinb5uvhjhn3lkj65zwomeu

Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis (+70 others)
2017 Bioinformatics  
The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their  ...  We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to  ...  Acknowledgements Members of the Quest for Orthologs Consortium: Adrian Altenhoff  ... 
doi:10.1093/bioinformatics/btx542 pmid:28968857 pmcid:PMC5860199 fatcat:drj7nplnqbg33gvao2zlzy3ui4

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  
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  ...  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 Quest for Orthologs Reference Proteomes are available for download in different formats: the protein sequences as FASTA and SeqXML files, CDS sequences for most proteins as FASTA files, and, for an  ... 
doi:10.1093/nar/gkaa308 pmid:32374845 pmcid:PMC7319555 fatcat:fuzbeoshlvegddgzcylkiwvqpu

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.  ...  We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017.  ...  Members of the Quest for Orthologs Consortium: Adrian Altenhoff, Judith A.  ... 
doi:10.1093/molbev/msz150 pmid:31241141 pmcid:PMC6759064 fatcat:ahhm3ev72nghlfyb5kfbjahnsu

Big Data Supervised Pairwise Ortholog Detection in Yeasts [chapter]

Deborah Galpert Cañizares, Sara del Río García, Francisco Herrera, Evys Ancede Gallardo, Agostinho Antunes, Guillermin Agüero-Chapin
2017 Yeast - Industrial Applications  
The efficiency and scalability of the calculation of these measures are analyzed to propose its implementation for big data.  ...  In conclusion, evaluated supervised algorithms that manage big and imbalanced data showed high effectiveness in Saccharomycete yeast genomes.  ...  The funders had no role in the study's design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.5772/intechopen.70479 fatcat:ohsspdtebzbnff46alosjlnmzu

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.  ...  This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological  ...  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

Making Sense of the Data

P. Donnelly
2011 Science  
But that is illusory: Data on human genetic diversity have proved to be a valuable tool in the quest to understand human biology. One example is recombination.  ...  When I began my career, I never imagined that someday I could simply look up a gene's coding sequence; fi nd its orthologs in other organisms; and order, from a service organization, a mutation to my specifi  ... 
doi:10.1126/science.1204089 pmid:21350160 fatcat:vwttovienzfuzmh2uz6catniu4

Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes

Eva S Deutekom, Berend Snel, Teunis J P van Dam
2020 Briefings in Bioinformatics  
Availability and implementation The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies  ...  Moreover, we compare the inferred orthologies to each other.  ...  Acknowledgements We would like to thank the developers of Ancestral Genomes, Xiaosong Huang and Paul Denis Thomas, for providing us with the additional data used in this study.  ... 
doi:10.1093/bib/bbaa206 pmid:32935832 pmcid:PMC8138875 fatcat:awmx3hla3nc7vcuk5ucmuda6le

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
2020 F1000Research  
The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative  ...  In this article, we provide a hands-on introduction to querying evolutionary data across several data sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European  ...  In particular, analysing evolutionary relationship data in RDF poses the following challenges: 1) complex data models -for example, while storing data in a hierarchical structure (HOGs) results in significant  ... 
doi:10.12688/f1000research.21027.2 fatcat:sdx3ddz2tvdtzeekyopsajasaa

A roadmap for global synthesis of the plant tree of life

Wolf L. Eiserhardt, Alexandre Antonelli, Dominic J. Bennett, Laura R. Botigué, J. Gordon Burleigh, Steven Dodsworth, Brian J. Enquist, Félix Forest, Jan T. Kim, Alexey M. Kozlov, Ilia J. Leitch, Brian S. Maitner (+11 others)
2018 American Journal of Botany  
However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers.  ...  Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts.  ...  For example, all-versus-all BLAST searching and clustering, a critical step in homology and orthology assessment, becomes computationally prohibitive as data increase.  ... 
doi:10.1002/ajb2.1041 pmid:29603138 fatcat:fykoyipup5hbtfmydcfvgxswxe

Comparing orthology methods and their performance by recapitulating patterns of eukaryotic genome evolution [article]

Eva S. Deutekom, Berend Snel, Teunis J.P. van Dam
2020 bioRxiv   pre-print
Moreover, we compare the inferred orthologies to each other.  ...  We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regards to genome evolution in eukaryotes.  ...  Acknowledgements We would like to thank the developers of Ancestral Genomes, Xiaosong Huang and Paul Denis Thomas, for providing us with the additional data used in this study.  ... 
doi:10.1101/2020.05.13.092791 fatcat:rnox4ojl6rd4nbovfz5jcnjlou

Inferring Orthology and Paralogy [chapter]

Adrian M. Altenhoff, Natasha M. Glover, Christophe Dessimoz
2019 Msphere  
In this chapter, we provide an overview of the methods used to infer orthology and paralogy.  ...  The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein  ...  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

NORTH: a highly accurate and scalable Naive Bayes based ORTHologous gene clustering algorithm [article]

Nabil Ibtehaz, Shafayat Ahmed, Bishwajit Saha, M. Sohel Rahman, Md. Shamsuzzoha Bayzid
2019 bioRxiv   pre-print
In this regard, identifying orthologous genes plays a pivotal role as the orthologous genes remain less diverged in the course of evolution.  ...  loss, introgression etc.), multiple paralogous genes, incomplete genome data, and for distantly related species where similarity is hard to recognize.  ...  Data availability Data used in this paper are available at KEGG (https://www.genome.jp/kegg/), and UniProt (https://www.uniprot.org/) databases.  ... 
doi:10.1101/528323 fatcat:amllzlhlunclpl3abunowrta6e

Birth and death of gene overlaps in vertebrates

Izabela Makałowska, Chiao-Feng Lin, Krisitina Hernandez
2007 BMC Evolutionary Biology  
Results: Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution.  ...  Conclusion: Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes  ...  Acknowledgements We gratefully thank Stephen Schaeffer for reading the manuscript and for his valuable comments, and Narayanan Veeraraghavan for his assistance.  ... 
doi:10.1186/1471-2148-7-193 pmid:17939861 pmcid:PMC2151771 fatcat:5myj26qvabcyrosybvbi3tt76e

Enabling Semantic Queries Across Federated Bioinformatics Databases [article]

Ana Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
2019 biorxiv/medrxiv   pre-print
However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.  ...  Similarly, the materialised RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint.  ...  for OMA, Bgee, and Core-IT.  ... 
doi:10.1101/686600 fatcat:ajkv2fmvzvbxje3kychiolirxm
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