Results 61 to 70 of about 2,351 (162)

Disk compression of k-mer sets

Algorithms for Molecular Biology, 2021
K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets.
Amatur Rahman, Rayan Chikhi, Paul Medvedev   +2 more
doaj   +1 more source

Whole genome sequencing of historical specimens from the world's largest fungal collection yields high‐quality assemblies

New Phytologist, Volume 251, Issue 2, Page 752-767, July 2026.
Summary High‐throughput molecular studies of museum specimens (museomics) have great potential in biodiversity research, but fungal historical collections have scarcely been examined, leading to no comprehensive methodological assessments. Here we present a whole genome sequencing (WGS) project conducted at the Fungarium of the Royal Botanic Gardens ...
Torda Varga, Roseina Woods, Frances Pitsillides, Rowena Hill, Alona Yu Biketova, Theo Llewellyn, Brandon J. P. Shaw, Emily Hodgson, Brigid Wong, Jasmine Le, Josepha Becker, Alexander J. Bradshaw, Seth L. E. Blake, Clementine Geeves, Quentin Levicky, Lottie Goodman, Ruben L. Mole, Sidney L. Reed, M. Carly Lin, Emily Read, Keenan Harris, Raquel Pino‐Bodas, László G. Nagy, Anna Bazzicalupo, Ester Gaya   +24 more
wiley   +1 more source

Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ

iScience, 2020
Summary: Pairwise whole-genome homology mapping is the problem of finding all pairs of homologous intervals between a pair of genomes. As the number of available whole genomes has been rising dramatically in the last few years, there has been a need for ...
Ilia Minkin, Paul Medvedev
doaj   +1 more source

Evolutionary Patterns of the Genes Involved in the Integrity and Segregation of Chromosomes in Sawflies (Hymenoptera: Symphyta)

Ecology and Evolution, Volume 16, Issue 6, June 2026.
This study identifies and characterizes the genes encoding cohesin and condensin complexes across Symphytan superfamilies, revealing their structural and functional roles with conserved motifs in maintaining genome stability. Phylogenetic analyses indicate that SMC genes originated from ancient duplication events, with notable gene loss (e.g., CAPG2 ...
Ayşe Rümeysa Nalça, Ertan Mahir Korkmaz   +1 more
wiley   +1 more source

Feature extraction methods for metagenome de Bruijn graphs collections based on samples classification information

Научно-технический вестник информационных технологий, механики и оптики
The paper considers the comparative analysis of metagenomic samples collections using de Bruijn graphs. We propose methods for automatic feature extraction based on the results of comparative sample analysis, expert metadata, and statistical tests to ...
A. B. Ivanov, A. A. Shalyto, V. I. Ulyantsev   +2 more
doaj   +1 more source

From short to long: The impact of read length on metagenome assembly and binning

Methods in Ecology and Evolution, Volume 17, Issue 6, Page 1788-1798, June 2026.
Abstract Metagenome sequencing not only plays a pivotal role in unravelling the genetic diversity and functional potential of microbial communities but also facilitates the discovery of genome context for microbial dark matter. This study presents a comparative analysis of metagenome sequencing strategies, focusing on the impact of read length on the ...
Xi Peng, Xingsheng Yang, Danrui Wang, Bo Zhao, Kai Feng, Qing He, Shang Wang, Ye Deng   +7 more
wiley   +1 more source

Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species

PROTEOMICS, Volume 26, Issue 5, Page 13-26, May 2026.
ABSTRACT Proteomics is strengthening research in biology and the diversification of the model organisms studied is very promising for fully understanding the complexity of biological principles. However, the lack of protein sequence databases for many species is a major bottleneck.
Adrien Brown, Alexandre Burel, Sarah Cianférani, Christine Carapito, Fabrice Bertile   +4 more
wiley   +1 more source

In‐and‐Out: Algorithmic Diffusion for Sampling Convex Bodies

Random Structures &Algorithms, Volume 68, Issue 3, May 2026.
ABSTRACT We present a new random walk for uniformly sampling high‐dimensional convex bodies. It achieves state‐of‐the‐art runtime complexity with stronger guarantees on the output than previously known, namely in Rényi divergence (which implies TV, 𝒲2, KL, χ2$$ {\chi}^2 $$).
Yunbum Kook, Santosh S. Vempala, Matthew S. Zhang   +2 more
wiley   +1 more source

Heights of Butterfly Trees

Random Structures &Algorithms, Volume 68, Issue 3, May 2026.
ABSTRACT Binary search trees (BSTs) are fundamental data structures whose performance is largely governed by tree height. We introduce a block model for constructing BSTs by embedding internal BSTs into the nodes of an external BST—a structure motivated by parallel data architectures—corresponding to composite permutations formed via Kronecker or ...
John Peca‐Medlin, Chenyang Zhong
wiley   +1 more source

Meta-colored Compacted de Bruijn Graphs

, 2023
Abstract Motivation The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods that perform read mapping or alignment, abundance estimation, and subsequent ...
Giulio Ermanno Pibiri, Jason Fan, Rob Patro   +2 more
openaire   +2 more sources