Results 51 to 60 of about 766,230 (330)

Optimal assembly for high throughput shotgun sequencing [PDF]

BMC Bioinformatics, 2013
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome.
Bresler, Guy, Bresler, Ma'ayan, Tse, David   +2 more
openaire   +6 more sources

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Microbiome, 2014
Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective ...
A. Fernandes, J. N. Reid, Jean M. Macklaim, T. A. McMurrough, D. Edgell, G. Gloor   +5 more
semanticscholar   +1 more source

High-Throughput Sequencing and Rare Genetic Diseases [PDF]

Molecular Syndromology, 2012
High-throughput sequencing has drastically changed the research of genes responsible for genetic disorders and is now gradually introduced as an additional genetic diagnostic testing in clinical practice. The current debates on the emerging technical, medical and ethical issues as well as the potential optimum use of the available technology are ...
Makrythanasis P, Antonarakis SE.
openaire   +3 more sources

HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing

Nucleic Acids Res., 2016
Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics.
H. Weissensteiner, D. Pacher, A. Kloss-Brandstätter, L. Forer, Günther Specht, H. Bandelt, F. Kronenberg, A. Salas, S. Schönherr   +8 more
semanticscholar   +1 more source

Small molecule regulators of microRNAs identified by high-throughput screen coupled with high-throughput sequencing

Nature Communications, 2023
MicroRNAs (miRNAs) regulate fundamental biological processes by silencing mRNA targets and are dysregulated in many diseases. Therefore, miRNA replacement or inhibition can be harnessed as potential therapeutics.
Lien D. Nguyen, Zhiyun Wei, M. Catarina Silva, Sergio Barberán-Soler, Jiarui Zhang, Rosalia Rabinovsky, Christina R. Muratore, Jonathan M. S. Stricker, Colin Hortman, Tracy L. Young-Pearse, Stephen J. Haggarty, Anna M. Krichevsky   +11 more
doaj   +1 more source

Phigaro: high-throughput prophage sequence annotation [PDF]

Bioinformatics, 2020
Abstract Summary Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated ‘prophage genome maps’ and marks possible transposon insertion spots inside prophages.
Elizaveta V Starikova, Polina O Tikhonova, Nikita A Prianichnikov, Chris M Rands, Evgeny M Zdobnov, Elena N Ilina, Vadim M Govorun   +6 more
openaire   +4 more sources

ReSeq simulates realistic Illumina high-throughput sequencing data

Genome Biology, 2021
In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project.
Stephan Schmeing, Mark D. Robinson
doaj   +1 more source

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment1

Applications in Plant Sciences, 2016
Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges.
Matthew G. Johnson, E. Gardner, Yang Liu, R. Medina, B. Goffinet, A. J. Shaw, N. Zerega, N. Wickett   +7 more
semanticscholar   +1 more source

Transcriptome-Wide High-Throughput m6A Sequencing of Differential m6A Methylation Patterns in the Human Rheumatoid Arthritis Fibroblast-Like Synoviocytes Cell Line MH7A

Journal of Inflammation Research, 2021
Hui Jiang1,2 *,* Kefeng Cao3 *,* Chang Fan,1,2 Xiaoya Cui,1,2 Yanzhen Ma,1,2 Jian Liu1 1Experimental Center of Clinical Research, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, People’s Republic of China; 2School ...
Jiang H, Cao K, Fan C, Cui X, Ma Y, Liu J   +5 more
doaj  

Tools for mapping high-throughput sequencing data [PDF]

Bioinformatics, 2012
Abstract Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial.
Johan Rung, Alvis Brazma, John C. Marioni, Nuno A. Fonseca   +3 more
openaire   +2 more sources