Data from: Integrating sequence evolution into probabilistic orthology analysis
Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs — stemming from a speciation — or paralogs — stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous re...
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Online Access: | https://doi.org/10.5061/dryad.4r910 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::b791418526b8c4c5caeb449da4a5bf10 2023-05-15T15:51:15+02:00 Data from: Integrating sequence evolution into probabilistic orthology analysis Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens 2015-07-07 https://doi.org/10.5061/dryad.4r910 undefined unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.4r910 http://dx.doi.org/10.5061/dryad.4r910 lic_creative-commons 10.5061/dryad.4r910 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89267 oai:easy.dans.knaw.nl:easy-dataset:89267 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Comparative genomics Phylogenetics Orthology Paralogy Sequence Evolution Gene Duplication Gene Loss Probabilistic Modeling Molecular Evolution Relaxed Molecular Clock Tree Reconciliation Tree Realization Homo sapiens Mus musculus Gallus gallus Taeniopygia guttata Canis lupus familiaris Monodelphis domestica Ciona intestinalis Danio rerio Ornithorhynchus anatinus Life sciences medicine and health care stat envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2015 fttriple https://doi.org/10.5061/dryad.4r910 2023-01-22T16:53:37Z Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs — stemming from a speciation — or paralogs — stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MRBAYESMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts. Supplementary Material for “Integrating Sequence Evolution into Probabilistic Orthology Analysis”This document contains the supplementary information including synthetic data parameters, figures, and tables for the paper “Integrating Sequence Evolution into Probabilistic Orthology Analysis”Supplementary_Material.pdf Dataset Canis lupus Unknown |
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Open Polar |
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Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Comparative genomics Phylogenetics Orthology Paralogy Sequence Evolution Gene Duplication Gene Loss Probabilistic Modeling Molecular Evolution Relaxed Molecular Clock Tree Reconciliation Tree Realization Homo sapiens Mus musculus Gallus gallus Taeniopygia guttata Canis lupus familiaris Monodelphis domestica Ciona intestinalis Danio rerio Ornithorhynchus anatinus Life sciences medicine and health care stat envir |
spellingShingle |
Comparative genomics Phylogenetics Orthology Paralogy Sequence Evolution Gene Duplication Gene Loss Probabilistic Modeling Molecular Evolution Relaxed Molecular Clock Tree Reconciliation Tree Realization Homo sapiens Mus musculus Gallus gallus Taeniopygia guttata Canis lupus familiaris Monodelphis domestica Ciona intestinalis Danio rerio Ornithorhynchus anatinus Life sciences medicine and health care stat envir Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens Data from: Integrating sequence evolution into probabilistic orthology analysis |
topic_facet |
Comparative genomics Phylogenetics Orthology Paralogy Sequence Evolution Gene Duplication Gene Loss Probabilistic Modeling Molecular Evolution Relaxed Molecular Clock Tree Reconciliation Tree Realization Homo sapiens Mus musculus Gallus gallus Taeniopygia guttata Canis lupus familiaris Monodelphis domestica Ciona intestinalis Danio rerio Ornithorhynchus anatinus Life sciences medicine and health care stat envir |
description |
Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs — stemming from a speciation — or paralogs — stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MRBAYESMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts. Supplementary Material for “Integrating Sequence Evolution into Probabilistic Orthology Analysis”This document contains the supplementary information including synthetic data parameters, figures, and tables for the paper “Integrating Sequence Evolution into Probabilistic Orthology Analysis”Supplementary_Material.pdf |
format |
Dataset |
author |
Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens |
author_facet |
Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens |
author_sort |
Ullah, Ikram |
title |
Data from: Integrating sequence evolution into probabilistic orthology analysis |
title_short |
Data from: Integrating sequence evolution into probabilistic orthology analysis |
title_full |
Data from: Integrating sequence evolution into probabilistic orthology analysis |
title_fullStr |
Data from: Integrating sequence evolution into probabilistic orthology analysis |
title_full_unstemmed |
Data from: Integrating sequence evolution into probabilistic orthology analysis |
title_sort |
data from: integrating sequence evolution into probabilistic orthology analysis |
publisher |
Dryad Digital Repository |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.4r910 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
10.5061/dryad.4r910 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89267 oai:easy.dans.knaw.nl:easy-dataset:89267 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
https://dx.doi.org/10.5061/dryad.4r910 http://dx.doi.org/10.5061/dryad.4r910 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.4r910 |
_version_ |
1766386374806601728 |