Zobrazeno 1 - 10
of 585
pro vyhledávání: '"k-mers"'
Autor:
Camille Moeckel, Manvita Mareboina, Maxwell A. Konnaris, Candace S.Y. Chan, Ioannis Mouratidis, Austin Montgomery, Nikol Chantzi, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 2289-2303 (2024)
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount
Externí odkaz:
https://doaj.org/article/c5c3dc95b94440cba3a1804c4060b067
Autor:
Jim Shaw, Yun William Yu
Publikováno v:
Microbiome, Vol 12, Iss 1, Pp 1-10 (2024)
Abstract Background Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenome-assembled genomes (MAGs). Contigs are linked by exploiting consistent signatures along a genome,
Externí odkaz:
https://doaj.org/article/f77300fb0b224c038718c4e822d9351d
Publikováno v:
Mycology, Pp 1-15 (2024)
Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-geno
Externí odkaz:
https://doaj.org/article/39a4f7f8f7984526a207bbf63c5f2878
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-23 (2024)
Abstract Computing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but they are often optimised for small k as a hash ta
Externí odkaz:
https://doaj.org/article/16986cd5151b494f8473d4024d0ad023
Publikováno v:
Applications in Plant Sciences, Vol 12, Iss 4, Pp n/a-n/a (2024)
Abstract Premise The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and e
Externí odkaz:
https://doaj.org/article/74119ba815f24708b7eba6da4d013319
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-21 (2024)
Abstract The problem of sequence identification or matching—determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence—is relevant for many important tasks in Computationa
Externí odkaz:
https://doaj.org/article/edf66e1b8cdf44abb9a00887e9b5d8c5
Autor:
Ioannis Mouratidis, Nikol Chantzi, Umair Khan, Maxwell A. Konnaris, Candace S. Y. Chan, Manvita Mareboina, Camille Moeckel, Ilias Georgakopoulos-Soares
Publikováno v:
BMC Genomics, Vol 24, Iss 1, Pp 1-13 (2023)
Abstract Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic stage where patients are past efficacious treatment periods and can result in less favorabl
Externí odkaz:
https://doaj.org/article/83e5bd9eb6b2423d8a916d016a86c015
Publikováno v:
Frontiers in Microbiology, Vol 15 (2024)
Traditional alignment-based methods meet serious challenges in genome sequence comparison and phylogeny reconstruction due to their high computational complexity. Here, we propose a new alignment-free method to analyze the phylogenetic relationships
Externí odkaz:
https://doaj.org/article/b32e1f93e89b46b48f793831f1f6c00b
Autor:
Sheinman, Michael
Publikováno v:
Известия высших учебных заведений: Прикладная нелинейная динамика, Vol 31, Iss 6, Pp 739-756 (2023)
The purpose of this article is to review usage of exact sequence matches in different field of genomic studies. Methods. The presentation is built in the form of a brief review of clearly non-exhaustive list of works in which the authors inferred bio
Externí odkaz:
https://doaj.org/article/044fbb3eb61d48739afccd80a6e5fd1d
Autor:
Wittler, Roland
Publikováno v:
Peer Community Journal, Vol 3, Iss , Pp - (2023)
To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and
Externí odkaz:
https://doaj.org/article/a463430ca95d4a17aa405c118a29ed58