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...
Main Authors: | , , , , |
---|---|
Format: | Dataset |
Language: | English |
Published: |
Dryad
2015
|
Subjects: | |
Online Access: | https://dx.doi.org/10.5061/dryad.4r910 https://datadryad.org/stash/dataset/doi:10.5061/dryad.4r910 |
id |
ftdatacite:10.5061/dryad.4r910 |
---|---|
record_format |
openpolar |
spelling |
ftdatacite:10.5061/dryad.4r910 2024-02-04T09:59:31+01:00 Data from: Integrating sequence evolution into probabilistic orthology analysis ... Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens 2015 https://dx.doi.org/10.5061/dryad.4r910 https://datadryad.org/stash/dataset/doi:10.5061/dryad.4r910 en eng Dryad https://dx.doi.org/10.1093/sysbio/syv044 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 Gene duplication Mus musculus Ciona intestinalis Ornithorhynchus anatinus Probabilistic Modeling Danio rerio Comparative genomics Homo Sapiens Tree Realization gene loss relaxed molecular clock orthology Tree Reconciliation Canis lupus familiaris Taeniopygia guttata paralogy Sequence Evolution Monodelphis domestica Gallus gallus Dataset dataset 2015 ftdatacite https://doi.org/10.5061/dryad.4r91010.1093/sysbio/syv044 2024-01-05T04:39:59Z 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 ... : 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 DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Gene duplication Mus musculus Ciona intestinalis Ornithorhynchus anatinus Probabilistic Modeling Danio rerio Comparative genomics Homo Sapiens Tree Realization gene loss relaxed molecular clock orthology Tree Reconciliation Canis lupus familiaris Taeniopygia guttata paralogy Sequence Evolution Monodelphis domestica Gallus gallus |
spellingShingle |
Gene duplication Mus musculus Ciona intestinalis Ornithorhynchus anatinus Probabilistic Modeling Danio rerio Comparative genomics Homo Sapiens Tree Realization gene loss relaxed molecular clock orthology Tree Reconciliation Canis lupus familiaris Taeniopygia guttata paralogy Sequence Evolution Monodelphis domestica Gallus gallus Ullah, Ikram Sjöstrand, Joel Andersson, Peter Sennblad, Bengt Lagergren, Jens Data from: Integrating sequence evolution into probabilistic orthology analysis ... |
topic_facet |
Gene duplication Mus musculus Ciona intestinalis Ornithorhynchus anatinus Probabilistic Modeling Danio rerio Comparative genomics Homo Sapiens Tree Realization gene loss relaxed molecular clock orthology Tree Reconciliation Canis lupus familiaris Taeniopygia guttata paralogy Sequence Evolution Monodelphis domestica Gallus gallus |
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 ... : 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 |
publishDate |
2015 |
url |
https://dx.doi.org/10.5061/dryad.4r910 https://datadryad.org/stash/dataset/doi:10.5061/dryad.4r910 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_relation |
https://dx.doi.org/10.1093/sysbio/syv044 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.4r91010.1093/sysbio/syv044 |
_version_ |
1789964371332431872 |