Results 1 to 10 of about 28,177 (251)

The Quest for Orthologs orthology benchmark service in 2022

Nucleic Acids Research, 2022
The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium.
Maria-Jesus Martin, Dmitry Repchevsky, David S Roos   +2 more
exaly   +14 more sources

Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration. [PDF]

J Mol Evol
The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthology plays a crucial role in understanding evolutionary
Majidian S, Hadziahmetovic A, Langschied F, Pascarelli S, Prieto-Baños S, Rojas-Vargas J, Quest for Orthologs Consortium, Braun EL, Dessimoz C, Diallo AB, Durand D, Fang G, Gabaldón T, Glover N, Liberles DA, McWhite C, Sonnhammer ELL, Thomas PD, Ouangraoua A, Julca I.   +19 more
europepmc   +2 more sources

Orthology Clusters from Gene Trees with Possvm

Molecular Biology and Evolution, 2021
Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL) is a tool that automates the process of classifying clusters of orthologous genes from precomputed phylogenetic trees.
Aida Ouangraoua, Arnau Sebé-Pedrós, Xavier Grau-Bové   +2 more
exaly   +2 more sources

A deep learning model for predicting essential proteins based on an attention mechanism [PDF]

Frontiers in Genetics
IntroductionEssential proteins are key to cellular viability, yet their experimental identification is costly and time-consuming.MethodsIn this study, DLAM is introduced as a deep learning framework that integrates four complementary biological cues ...
Shunxian Zhou, Haodong Zhou, Sisi Chen, Yangtai Xu, Lei Wang   +4 more
doaj   +2 more sources

Annotation matters: the effect of structural gene annotation on orthology inference. [PDF]

Bioinformatics
Motivation In silico gene annotation, the process of identifying the genes present in a genome, remains a challenging task. As genome assemblies rapidly increase, the corresponding gene models and repertoires often fall short in quality. Despite advances
Prieto-Baños S, Nevers Y, Altenhoff A, Warwick Vesztrocy A, Dessimoz C, Glover NM.   +5 more
europepmc   +2 more sources

Domainoid: domain-oriented orthology inference

BMC Bioinformatics, 2019
Background Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains.
Emma Persson, Mateusz Kaduk, Sofia K. Forslund, Erik L. L. Sonnhammer   +3 more
doaj   +2 more sources

Orthology and near-cographs in the context of phylogenetic networks [PDF]

Algorithms for Molecular Biology
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying gene or ...
Anna Lindeberg, Guillaume E. Scholz, Nicolas Wieseke, Marc Hellmuth   +3 more
doaj   +2 more sources

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

bioRxiv
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specifically, we show that enhanced phylogenetic delineation of
Emms DM, Liu Y, Belcher L, Holmes J, Kelly S.   +4 more
europepmc   +2 more sources

Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

Applications in Plant Sciences
Premise Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses.
Irène Liao, Lachezar Nikolov
exaly   +2 more sources

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

bioRxiv, 2021
Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales.
C. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunic, P. Bork, J. Huerta-Cepas   +4 more
semanticscholar   +1 more source