Results 31 to 40 of about 30,147 (189)

Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

mSystems, 2023
Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation.
Mary Maranga, Pawel Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijevic, Chris Chandler, Richard Bonneau, Ramnik J. Xavier, Tommi Vatanen, Tomasz Kosciolek   +8 more
doaj   +1 more source

Perspectives on Orthology During the Quest for Orthologs. [PDF]

J Mol Evol
Abstract This special issue from the Quest for Orthologs community highlights ongoing challenges in detecting and characterizing orthologous genes in the annotation of protein functions. Eleven articles are presented describing ongoing research in this area.
Glover N, Liberles DA.
europepmc   +4 more sources

Orthology: Promises and Challenges [PDF]

, 2020
Orthology is a cornerstone of comparative genomics and has numerous applications in current biology. In this chapter, we first introduce the concepts of orthology and paralogy. We then present the currently available orthology inference methods and the community-led efforts of standardization and benchmarking accompanying these developments.
Nevers, Yannis, Defosset, Audrey, Lecompte, Odile   +2 more
openaire   +2 more sources

Detecting putative orthologs [PDF]

Bioinformatics, 2003
Abstract Summary: We developed an algorithm that improves upon the common procedure of taking reciprocal best blast hits (rbh) in the identification of orthologs. The method—reciprocal smallest distance algorithm (rsd)—relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs ...
Dennis P. Wall, H. B. Fraser, A. E. Hirsh   +2 more
openaire   +3 more sources

Representatives of orthology groups

, 2015
Representatives of orthology ...
Emma L. Rhule (3321072), Murray, Gemma G. R., Rhule, Emma L., Weinert, Lucy A., Gemma G. R. Murray (3299280), Welch, John J., John J. Welch (109918), Lucy A. Weinert (109914)   +7 more
core   +1 more source

CGP orthology clustering

, 2020
Orthology clustering set used on the Caenorhabditis Genomes Project (CGP) website (caenorhabditis.org). This dataset was generated using longest-isoform-filtered proteins from sequenced Caenorhabditis species and Orthofinder (see https://github.com ...
Lewis Stevens
core   +1 more source

Rhizobiales-assigned draft genome orthology matrix

, 2019
Table describing gene orthology between all draft and finished Mesorhizobium genomes determined to be of sufficient quality for species assignments.
Alex Greenlon (6690500)
core   +1 more source

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer

eLife, 2019
Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans.
Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode   +3 more
doaj   +1 more source

Rickettsia gene orthology groups - presence/absence data

, 2015
Rickettsia gene orthology groups - presence/absence ...
Emma L. Rhule (3321072), Gemma G. R. Murray (3299280), John J. Welch (109918), Lucy A. Weinert (109914)   +3 more
core   +1 more source

The Ortholog Conjecture Revisited: the Value of Orthologs and Paralogs in Function Prediction [PDF]

Bioinformatics, 2019
Abstract The computational prediction of gene function is a key step in making full use of newly sequenced genomes. Function is generally predicted by transferring annotations from homologous genes or proteins for which experimental evidence exists.
Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac   +3 more
openaire   +2 more sources