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Analysis of RNA Sequences and Modifications Using NASE
2023Mass spectrometry is an ideal method for the discovery and characterization of modified RNAs. Unlike other traditional sequencing methods, mass spectrometry can identify and localize multiple types of modifications in tandem. One of the traditional hurdles to using this powerful technique has been a paucity of software to interpret the complicated data
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Analysis of AmpliSeq RNA-Sequencing Enrichment Panels
2015This study presents a proof of concept of encoding genomic signatures in the AmpliSeq technology. The samples of patients with a disease and healthy ones have been processed using an AmpliSeq RNA sequencing kit of a custom design, that include 290 amplicons, sequenced using an IonTorrent machine. The read count data show the sufficient coverage in most
Marek S. Wiewiórka +2 more
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Borrelia burgdorferi Transcriptome Analysis by RNA-Sequencing
2017Next-Generation Sequencing (NGS) has revolutionized transcriptomics studies in the last decade. Transcriptome analysis experiments using NGS-based RNA-sequencing have several advantages over DNA microarray analysis. Novel unannotated transcripts and transcriptional start sites can be identified.
M, Lybecker, K C, Henderson
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RNA Sequencing: From Sample Preparation to Analysis
2014The introduction of RNA sequencing (RNA-seq), as a direct result of rapid progression of next-generation sequencing technologies, has revolutionized the world of transcriptomics. It enables quantification of the complete set of RNA with all its isoforms in a given cell, in far greater accuracy than before.
Sho, Maekawa +3 more
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Analysis of ribosomal RNA sequences by combinatorial clustering.
Proceedings. International Conference on Intelligent Systems for Molecular Biology, 2000We present an analysis of multi-aligned eukaryotic and procaryotic small subunit rRNA sequences using a novel segmentation and clustering procedure capable of extracting subsets of sequences that share common sequence features. This procedure consists of: i) segmentation of aligned sequences using a dynamic programming procedure, and subsequent ...
Poe Xing +6 more
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Pichia pastoris RNA-Sequencing and Data Analysis
RNA sequencing (RNA-seq) allows for transcriptome profiling, usually with the goal of comparing the gene expression between conditions of interest. Transcriptome profiling helped to understand and improve the use of microbes in industrial processes, as exemplified numerous times for the biotechnologically relevant yeast Komagataella phaffii.Julian Christopher, Krappinger +4 more
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Markov analysis of viral DNA/RNA sequences
Journal of Theoretical Biology, 1980Abstract This work applies a previously published method for determining the order of a Markov chain to the DNA/RNA sequences of φX174, SV40 and MS2. In the first two cases rather long-range order is found—third and second order respectively—but zero order is the appropriate model for MS2.
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High-throughput biochemistry in RNA sequence space: predicting structure and function
Nature Reviews Genetics, 2023Emil Marklund +2 more
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RNA 5-Methylcytosine Analysis by Bisulfite Sequencing
2015Cells have developed molecular machineries, which can chemically modify DNA and RNA nucleosides. One particular and chemically simple modification, (cytosine-5) methylation (m(5)C), has been detected both in RNA and DNA suggesting universal use of m(5)C for the function of these nucleotide polymers.
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RNA sequencing and transcriptome analysis
2020Elizabeth D. Au, Michael H. Farkas
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