Results 11 to 20 of about 2,656 (123)
Molecular Ecology Resources, 2022 Abstract Whole‐genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In
Daniel Tello +13 more
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Basis reduction for cryptogroups and orthogroups [PDF]
Semigroup Forum, 2020 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Casimiro, Ana, Skapinakis, Eduardo
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Hyperdecidability of pseudovarieties of orthogroups [PDF]
Glasgow Mathematical Journal, 2001 Let W denote the intersection with the pseudovariety of completely regular semigroups of the Mal'cev product of the pseudovariety of bands with a pseudovariety V of completely regular semigroups. It is shown that the (pseudo)word problem for W is reduced to that for V in such a way that decidability is preserved in the case in which terms involving ...
Almeida, Jorge, Trotter, Peter G.
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OrthoML2GO: homology-based protein function prediction using orthogroups and machine learning. [PDF]
Vavilovskii Zhurnal Genet SelektsiiIn recent years, the rapid growth of sequencing data has exacerbated the problem of functional annotation of protein sequences, as traditional homology-based methods face limitations when working with distant homologs, making it difficult to accurately determine protein functions.
Malyugin EV, Afonnikov DA.
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ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa [PDF]
Molecular Biology and Evolution, 2018 Web tool: We developed a web tool named ORTHOSCOPE to identify orthogroups of specific molecules within major bilaterian lineages. ORTHOSCOPE allows users to employ several sequences of a specific molecule and a user-specified species tree as queries. A test analysis using data from 36 bilaterians was accomplished within 140 seconds.
Jun Inoue, Noriyuki Satoh
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Methods in Ecology and Evolution, 2023 Abstract Transcriptome sequencing technologies have revolutionized the field of phylogenomics by facilitating the identification of homologous genes for species without whole genome sequences.
Jingting Shen +3 more
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Phylogenetic analyses for orthogroup-based classification of GDSL-type esterase/lipase (GELP) family in angiosperm representative species [PDF]
, 2021 Abstract GDSL-type esterase/lipase (GELP) enzymes have multiple functions in plants, spanning from developmental processes to the response to biotic and abiotic stresses. Genes encoding GELP belong to a large gene family with several tens to more than hundred members per angiosperm species.
Cenci Alberto +3 more
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy [PDF]
Genome Biology, 2015 AbstractIdentifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy.
Emms, D, Kelly, S
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Supplemental Dataset for, "Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench"
, 2020 The supplemental dataset for, "Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench"
Emms, David, Kelly, Steven
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Methods in Ecology and Evolution, 2020 AbstractIdentification of homology relationships is essential for inferring gene functions, detecting phylogeny of gene families, discovering evolutionary history of life, and usually, is the first step of many genetic and genomic studies. However, the presence of gene duplicates, variation on evolutionary rates of homologs, fusion and fission of genes,
Shengyu Zhou +3 more
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