Results 21 to 30 of about 789,685 (173)
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 +13 more
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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 +4 more
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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 +13 more
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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 +2 more
openaire +3 more sources
Base Sequence Context Effects on Nucleotide Excision Repair
Journal of Nucleic Acids, 2010 Nucleotide excision repair (NER) plays a critical role in maintaining the integrity of the genome when damaged by bulky DNA lesions, since inefficient repair can cause mutations and human diseases notably cancer. The structural properties of DNA lesions
Yuqin Cai +3 more
doaj +1 more source
Application of Sequence Embedding in Protein Sequence-Based Predictions [PDF]
arXiv, 2021 In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in natural language processing, several applications of sequence embedding have been observed.
arxiv
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 +3 more
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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 +5 more
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On a construction method of new moment sequences [PDF]
arXiv, 2023 In this paper we provide a way to construct new moment sequences from a given moment sequence. An operator based on multivariate positive polynomials is applied to get the new moment sequences. A class of new sequences is corresponding to a unique symmetric polynomial; if this polynomial is positive, then the new sequence becomes again a moment ...
arxiv
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 +4 more
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