Results 11 to 20 of about 4,265 (160)
Methods in Ecology and Evolution, 2023 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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OrthoML2GO: homology-based protein function prediction using orthogroups and machine learning
Вавиловский журнал генетики и селекцииIn 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 ...
E. V. Malyugin, D. A. Afonnikov
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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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Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench [PDF]
Genome Biology and Evolution, 2020 Abstract Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert-curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup inference.
Emms, DM, Kelly, S
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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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BMC Research Notes, 2021 Objectives Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms.
Mick Van Vlierberghe +2 more
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Plant Communications, 2023 Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However,
Zhen Zeng +6 more
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A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)
GigaByte, 2022 The apple cultivar ‘Honeycrisp’ has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent.
Awais Khan +7 more
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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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Identification and analysis of the secretome of plant pathogenic fungi reveals lifestyle adaptation
Frontiers in Microbiology, 2023 The secretory proteome plays an important role in the pathogenesis of phytopathogenic fungi. However, the relationship between the large-scale secretome of phytopathogenic fungi and their lifestyle is not fully understood.
Mingxuan Jia +18 more
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