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Indexing and searching petabase-scale nucleotide resources
Searching vast and rapidly growing nucleotide content in resources, such as runs in the Sequence Read Archive and assemblies for whole-genome shotgun...
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Habitable Zone in Nucleotide Composition Space: Phase Diagram of Life
We plotted the whole-genome sequences of many organisms in nucleotide composition space. As a result, all genome sequences were distributed in a very...
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DNA Sequence Assembly and Annotation of Genes
This chapter describes the different sequencing strategies, the pros and cons of the different strategies to help you select the optimal DNA...
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Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution
Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression....
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Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
Biological sequence classification is vital in various fields, such as genomics and bioinformatics. The advancement and reduced cost of genomic...
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Karyotype and Nucleotide Sequence of COI Gene of Chironomus sororius Wülker, 1973 (Diptera, Chironomidae) from the Pechora River Delta
Abstract—The larva of Chironomus sororius Wülker 1973 was for the first time found in the European part of Russia and above the Arctic Circle, in...
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Derived Polymorphic Amplified Cleaved Sequence (dPACS) Assay
The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism...
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SNPD-CRISPR: Single Nucleotide Polymorphism-Distinguishable Repression or Enhancement of a Target Gene Expression by CRISPR System
A wide range of diseases, including cancer, autoimmune diseases, or neurodegenerative diseases, have been associated with single nucleotide mutations...
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Complete nucleotide sequence of a divergent variant of grapevine fabavirus from northeastern China
Grapevine fabavirus (GFabV) was identified in the ‘**angfei’ grapevine in Liaoning, China, by small RNA sequencing. The complete nucleotide sequences...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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Single-Nucleotide Polymorphism
In forensic analysis, the conventional short tandem repeat (STR) markers are routinely used for examination of the biological samples. But, in the...
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The nearly complete genome sequence of clade B, wheat streak mosaic virus isolate from Türkiye
Wheat streak mosaic virus is one of the most widespread viruses in cereal crops, causing severe losses and dramatically affecting worldwide wheat...
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Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel
Cyclic nucleotide-gated ion channels are crucial in many physiological processes such as vision and pacemaking in the heart. SthK is a prokaryotic...
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Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing...
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Influence of Nucleotide Context on Non-Specific Amplification of DNA with Bst exo– DNA Polymerase
AbstractIsothermal nucleic acids amplification that requires DNA polymerases with strand-displacement activity gained more attention in the last two...
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Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism
Therapeutic prime editing of hematopoietic stem and progenitor cells (HSPCs) holds great potential to remedy blood disorders. Quiescent cells have...
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Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny
BackgroundSince DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided...
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Sequence-Based Classification and Identification
You will be introduced to the classification of prokaryotes from species to the higher levels of class and phyla. You will learn that the 16S rRNA...
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Methods for Assessment of Nucleotide Excision Repair Efficiency
AbstractNucleotide excision repair (NER) is responsible for removing a wide variety of bulky adducts from DNA, thus contributing to the maintenance...
