Results 21 to 30 of about 842,010 (246)

Local alignment of generalized k-base encoded DNA sequence

BMC Bioinformatics, 2010
Background DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base ...
Nelson Stanley F, Homer Nils, Merriman Barry   +2 more
doaj   +1 more source

DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing

Nature Communications, 2023
There is a need to improve and expand mitochondrial base editing tools. Here the authors identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in dsDNA; they develop cytosine base editors and introduce mutations at ...
Li Mi, Ming Shi, Yu-Xuan Li, Gang Xie, Xichen Rao, Damu Wu, Aimin Cheng, Mengxiao Niu, Fengli Xu, Ying Yu, Ning Gao, Wensheng Wei, Xianhua Wang, Yangming Wang   +13 more
doaj   +1 more source

Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration

Life, 2022
DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike ...
Robert T. Young, Luke Czapla, Zoe O. Wefers, Benjamin M. Cohen, Wilma K. Olson   +4 more
doaj   +1 more source

Synthesis and Evaluation of MGB Polyamide-Oligonucleotide Conjugates as Gene Expression Control Compounds

Journal of Nucleic Acids, 2023
MGB polyamide-oligonucleotide conjugates ON 1-4 with linked MGB polyamides at the 2-exocyclic amino group of a guanine base using aminoalkyl linkers were synthesized and evaluated in terms of binding affinity for complementary DNA containing the MGB ...
Kazuo Kamaike, Mutsumi Sano, Daisuke Sakata, Yu Nishihara, Hiroaki Amino, Akihiro Ohtsuki, Yui Okada, Takafumi Miyakawa, Makoto Kogawara, Mai Tsutsumi, Misato Takahashi, Etsuko Kawashima, Koichiro Ota, Hiroaki Miyaoka   +13 more
doaj   +1 more source

Sequence-based pangenomic core detection

iScience, 2022
One of the most basic kinds of analysis to be performed on a pangenome is the detection of its core, i.e., the information shared among all members. Pangenomic core detection is classically done on the gene level and many tools focus exclusively on core detection in prokaryotes. Here, we present a new method for sequence-based pangenomic core detection.
Schulz, Tizian, Wittler, Roland, Stoye, Jens   +2 more
openaire   +3 more sources

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

eLife, 2013
Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be ...
Zhi Qi, Robert A Pugh, Maria Spies, Yann R Chemla   +3 more
doaj   +1 more source

Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Viruses, 2018
Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves ...
Shin-Lin Tu, Jeannette P. Staheli, Colum McClay, Kathleen McLeod, Timothy M. Rose, Chris Upton   +5 more
doaj   +1 more source

Effect of Base Sequence on G-Wire Formation in Solution

Journal of Nucleic Acids, 2010
The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE).
Lea Spindler, Martin Rigler, Irena Drevenšek-Olenik, Nason Ma'ani Hessari, Mateus Webba da Silva   +4 more
doaj   +1 more source

Peak Height Pattern in Dichloro-Rhodamine and Energy Transfer Dye Terminator Sequencing

BioTechniques, 1998
Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing.
H. Zakeri, G. Amparo, S.-M. Chen, S. Spurgeon, P.-Y. Kwok   +4 more
doaj   +1 more source

Phenotypic and Molecular Characterization of Multidrug-Resistant Clinical Isolates of the Candidozyma haemuli Species Complex (Formerly Candida haemulonii Species Complex) from the Brazilian Amazon Reveals the First Case of Candidozyma pseudohaemuli in Brazil

Journal of Fungi
This study included 24 isolates of the Candidozyma haemuli species complex from patients in the Brazilian Amazon between 2021 and 2024. These isolates were identified by sequencing as C. duobushaemuli (54.2%), C. haemuli sensu stricto (29.2%), C. haemuli
Sérgio Lobato França, Rodrigo Santos de Oliveira, Gabriel Silas Marinho Sousa, Sarah Rodrigues de Sá, Walber da Silva Nogueira, Elaine Patrícia Tavares do Espírito Santo, Daniel dos Santos Caldas, Silvia Helena Marques da Silva   +7 more
doaj   +1 more source