Results 51 to 60 of about 111,403 (262)

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.

PLoS ONE, 2020
The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes.
Agnes Scheunert, Marco Dorfner, Thomas Lingl, Christoph Oberprieler   +3 more
doaj   +1 more source

Dual native G‐quadruplex folding is associated with chromatin looping at the MYC locus

FEBS Open Bio, EarlyView.
BG4‐detectable G‐quadruplex (G4) in HaCaT and NHEK keratinocytes identified folded and unfolded G4s enriched at promoters/TSSs and active enhancers, whereas unfolded G4s also overlapped weak/poised enhancers. At MYC–PVT1, 3C‐qPCR detected enhancer–promoter looping only when G4s were simultaneously folded at both regulatory elements under native ...
Dieila Giomo de Lima, Gustavo Narvaes Guimarães, Emilyane de Oliveira Santana Amaral, Bianca Caroline Figueiredo Bianco, Manuel Jara‐Espejo, Sérgio Roberto Peres Line, Ana Paula de Souza, Aline Cristiane Planello   +7 more
wiley   +1 more source

A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats [PDF]

BioMed Research International, 2014
Background. Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses.
Lian, Shuaibin, Li, Qingyan, Dai, Zhiming, Xiang, Qian, Dai, Xianhua   +4 more
openaire   +2 more sources

A comparative evaluation of genome assembly reconciliation tools

Genome Biology, 2017
Background The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific ...
Hind Alhakami, Hamid Mirebrahim, Stefano Lonardi   +2 more
doaj   +1 more source

Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish

FEBS Open Bio, EarlyView.
The presence of biotin‐binding avidin proteins in fish and their biological significance are poorly characterized. We cataloged fish avidins and demonstrate that they are widely present and evolutionarily conserved. We created avd knockout zebrafish and show that zebavidin is dispensable for development and that resistance of avd knockout embryos in ...
Anni K. Saralahti, Markus J. T. Ojanen, Mataleena Parikka, Otto Kauko, Mika Rämet, Vesa P. Hytönen   +5 more
wiley   +1 more source

Nicotiana glauca whole-genome investigation for cT-DNA study

BMC Research Notes, 2018
Objective Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest.
Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatiana Matveeva   +3 more
doaj   +1 more source

Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm

Frontiers in Cellular and Infection Microbiology, 2021
BackgroundEmerging long reads sequencing technology has greatly changed the landscape of whole-genome sequencing, enabling scientists to contribute to decoding the genetic information of non-model species.
Jinming Wang, Kai Chen, Qiaoyun Ren, Ying Zhang, Junlong Liu, Guangying Wang, Aihong Liu, Youquan Li, Guangyuan Liu, Jianxun Luo, Wei Miao, Jie Xiong, Hong Yin, Hong Yin, Guiquan Guan   +14 more
doaj   +1 more source

RNA Sequencing Resolves Cryptic Pathogenic Variants in Mitochondrial Disease

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Mitochondrial diseases are the most common inherited metabolic disorders, characterized by pronounced clinical and genetic heterogeneity that complicates molecular diagnosis. Although DNA‐based sequencing approaches have become standard in genetic testing, up to half of patients remain without a definitive diagnosis.
Zhimei Liu, Xin Duan, Fatemeh Peymani, Jia Wang, Chengjia Bao, Chaolong Xu, Ying Zou, Zixuan Zhang, Yunxi Zhang, Tongyue Li, Martin Pavlov, Junling Wang, Minhan Song, Tianyu Song, Xiaodi Han, Mingxi Sun, Danmin Shen, Ruoyu Duan, Huafang Jiang, Manting Xu, Holger Prokisch, Fang Fang   +21 more
wiley   +1 more source

Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome. [PDF]

PLoS ONE, 2015
Transcriptomes are one of the first sources of high-throughput genomic data that have benefitted from the introduction of Next-Gen Sequencing. As sequencing technology becomes more accessible, transcriptome sequencing is applicable to multiple organisms ...
Andrey Ptitsyn, Ramzi Temanni, Christelle Bouchard, Peter A V Anderson   +3 more
doaj   +1 more source

Prominent Movement Disorders in RNU2‐2‐Related Spliceosomopathy

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Pediatric movement disorders often overlap with neurodevelopmental diseases, suggesting shared molecular mechanisms. Variants in small nuclear RNA (snRNA) genes encoding spliceosome components have recently been associated with neurodevelopmental disorders, termed “RNUopathies.” We analyzed genome sequencing data from 14 patients with ...
Magdalena Krygier, Ugo Sorrentino, Matias Wagner, Marta Zawadzka, Anna Lemska, Maria Mazurkiewicz‐Bełdzińska, Michael Zech   +6 more
wiley   +1 more source