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Bioinformatics Analysis of miRNA Sequencing Data
The bioinformatics analysis of miRNA is a complicated task with multiple operations and steps involved from processing of raw sequence data to...
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COSAP: Comparative Sequencing Analysis Platform
BackgroundRecent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short...
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Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed...
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Next Generation Sequencing in Healthcare
With the fast development and broad application of next-generation sequencing (NGS) technology, data on genomic sequences is now reaching the aims of...
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Differential Poly(A) Tail Length Analysis Using Nanopore Sequencing
The poly(A) tail is a sequence of several adenosine nucleotides added to the 3′ end of RNA molecules transcribed by polymerase II. The dynamics of...
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Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications,...
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Application of Deep Sequencing in Phage Display
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the...
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Species Identification Through Sequencing
Ciliates with nuclear dualism are reported to be a highly divergent unicellular eukaryotes. They play very vital roles in regulation of microbial...
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Single-cell RNA sequencing integrated with bulk RNA sequencing analysis identifies a tumor immune microenvironment-related lncRNA signature in lung adenocarcinoma
BackgroundRecently, long non-coding RNAs (lncRNAs) have been demonstrated as essential roles in tumor immune microenvironments (TIME). Nevertheless,...
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TILLING by Sequencing
The Targeting Induced Local Lesions In Genome (TILLING) is emerging as a preferred technique of reverse genetics. The use of next generation...
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Nanopore-Mediated Sequencing of Circular RNA
Circular RNAs (circRNAs) constitute a group of RNAs defined by a covalent bond between the 5′ and 3′ end formed by a unique back-splicing event. Most...
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Amplicon Sequencing Pipelines in Metagenomics
Taxonomic profiling among a large number of samples is a fundamental task during amplicon sequencing analysis. The heterogeneity and technical noises...
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Exome Sequencing
Exome sequencing, also known as whole exome sequencing (WES or WXS), is a technique for sequencing all the expressed genes in a genome (known as the...
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Mitochondrial DNA Sequencing and Heteroplasmy Quantification by Next Generation Sequencing
Over the last 10 years, next generation sequencing (NGS) became the gold standard for both diagnosis and discovery of new disease genes responsible...
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Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores
This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing...
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Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail...
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Nanopore Sequencing for Mixed Samples
Long read Nanopore sequencing can be utilised to determine the quality and accuracy of genetically engineered changes in animals, which often produce...
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Next-Generation Bisulfite Sequencing for Targeted DNA Methylation Analysis
Bisulfite sequencing is the “gold-standard” technique for DNA methylation analysis. By combining bisulfite sequencing with high-throughput,...
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16S rRNA Amplicon Sequencing
The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The...
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Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons
Fungal species participate in vast numbers of processes in the landscape around us. However, their cryptic mycelial growth, inside various substrates...