Results 51 to 60 of about 30,147 (189)

Identification of mammalian orthologs using local synteny

BMC Genomics, 2009
Background Accurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication, and high rates of ...
Nelson Craig E, Mandoiu Ion I, Jun Jin
doaj   +1 more source

The Orthologic of Epistemic Modals

Journal of Philosophical Logic
Minor edits for final version forthcoming in Journal of Philosophical ...
Wesley H. Holliday, Matthew Mandelkern
openaire   +5 more sources

Avian MHC Evolution in the Era of Genomics: Phase 1.0

Cells, 2019
Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest.
Emily A. O’Connor, Helena Westerdahl, Reto Burri, Scott V. Edwards   +3 more
doaj   +1 more source

Standardized benchmarking in the quest for orthologs [PDF]

Nature Methods, 2016
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision–recall trade-offs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C   +27 more
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Scripts to help orthology prediction and selection analysis

, 2016
<p>Initial release of the orthology and selection helper scripts.</p ...
Daniel Elsner (3267894), Daniel Elsner
core   +1 more source

Advances and Applications in the Quest for Orthologs [PDF]

Molecular Biology and Evolution, 2019
AbstractGene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses.
Glover, Natasha, Dessimoz, Christophe, Ebersberger, Ingo, Forslund, Sofia, Gabaldon, Toni, Huerta-Cepas, Jaime, Martin, Maria J, Muffato, Matthieu, Patricio, Mateus, Pereira, C., Sousa da Silva, A., Wang, Yan, The Quest For Orthologs Consortium, Qfo, Lecompte, Odile, Hurstel, Alexandre, Sonnhammer, Erik, Thomas, Paul D   +16 more
openaire   +9 more sources

On the consistency of orthology relationships

BMC Bioinformatics, 2016
Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/paralogy relationships [Formula: see text] on a ...
Jones, Mark, Paul, Christophe, Scornavacca, Celine   +2 more
openaire   +3 more sources

An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome

Frontiers in Plant Science, 2018
Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement.
Hongtao Song, Kui Lin, Jinglu Hu, Erli Pang   +3 more
doaj   +1 more source

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. [PDF]

PLoS ONE, 2013
The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference
Daniel A Dalquen, Adrian M Altenhoff, Gaston H Gonnet, Christophe Dessimoz   +3 more
doaj   +1 more source

Integrating Sequence Evolution into Probabilistic Orthology Analysis

, 2015
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 ...
Lagergren, Jens, Ullah, Ikram, Ullah, Ikram,, Sennblad, Bengt, Lagergren, Jens,, Sjöstrand, Joel, Andersson, Peter, Sjöstrand, Joel,, Andersson, Peter,, Lagergren, J, Sennblad, B,, Sjostrand, J, Andersson, P, Ullah, I,   +13 more
core   +1 more source