Results 21 to 30 of about 262,017 (266)

Nucleotide sequence-directed mapping of the nucleosomes

Nucleic Acids Research, 1983
The concept of sequence-dependent deformational anisotropy of DNA proposed earlier is further elaborated and a computational procedure is developed for the sequence-directed mapping of the nucleosomes along chromatin DNA nucleotide sequences. The deformational anisotropy is found to be nonuniform along the molecule of the nucleosomal DNA, suggesting ...
G, Mengeritsky, E N, Trifonov
openaire   +3 more sources

Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA

PLoS Biology, 2022
Dihydrouridine is a modified nucleotide universally present in tRNAs, but the complete dihydrouridine landscape is unknown in any organism. We introduce dihydrouridine sequencing (D-seq) for transcriptome-wide mapping of D with single-nucleotide ...
Austin S. Draycott, Cassandra Schaening-Burgos, Maria F. Rojas-Duran, Loren Wilson, Leonard Schärfen, Karla M. Neugebauer, Sigrid Nachtergaele, Wendy V. Gilbert   +7 more
doaj  

Design of microsatellite markers for Schizophyllum commune (Agaricales, Basidiomycota) based on analysis of its genome

Ukrainian Botanical Journal, 2022
Simple sequence repeats of DNA (SSRs) are the most popular source of genetic markers used in population genetics, phylogenetics, and genetic mapping. A large number of nucleotide repeats enriched in G and C were identified. 336 mononucleotide motifs with
Boiko S.M.
doaj   +1 more source

Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map [PDF]

Nature Protocols, 2020
ABSTRACTRibose-Map is a user-friendly, standardized bioinformatics toolkit for the comprehensive analysis of ribonucleotide sequencing experiments. It allows researchers to map the locations of ribonucleotides in DNA to single-nucleotide resolution and identify biological signatures of ribonucleotide incorporation.
Alli L. Gombolay, Francesca Storici
openaire   +2 more sources

Use of Denaturing HPLC to Map Human and Murine Genes and to Validate Single-Nucleotide Polymorphisms

BioTechniques, 2000
Linkage mapping has been extensively applied in the murine and human genomes. It remains a powerful approach to mapping genes and identifying genetic variants.
Lynn M. Schriml, Raymond J. Peterson, Bernard Gerrard, Michael Dean   +3 more
doaj   +1 more source

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

BMC Bioinformatics, 2019
Background Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes.
Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder   +6 more
doaj   +1 more source

NMR Studies of Retroviral Genome Packaging

Viruses, 2020
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs.
Patricia S. Boyd, Janae B. Brown, Joshua D. Brown, Jonathan Catazaro, Issac Chaudry, Pengfei Ding, Xinmei Dong, Jan Marchant, Colin T. O’Hern, Karndeep Singh, Canessa Swanson, Michael F. Summers, Saif Yasin   +12 more
doaj   +1 more source

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

BMC Genomics, 2017
Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference.
Peng Zhou, Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge, Nevin D. Young   +12 more
doaj   +1 more source

Epitranscriptomic mapping of RNA modifications at single-nucleotide resolution using rhodamine sequencing (Rho-seq)

STAR Protocols, 2022
Summary: The recent development of epitranscriptomics revealed a new fundamental layer of gene expression, but the mapping of most RNA modifications remains technically challenging. Here, we describe our protocol for Rho-Seq, which enables the mapping of
Olivier Finet, Carlo Yague-Sanz, Damien Hermand   +2 more
doaj   +1 more source

Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

Genome Biology
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood.
Niko Popitsch, Tobias Neumann, Arndt von Haeseler, Stefan L. Ameres   +3 more
doaj   +1 more source