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In Silico Analysis of Micro-RNA Sequencing Data
2021High-throughput sequencing for micro-RNAs (miRNAs) to obtain expression estimates is a central method of molecular biology. Surprisingly, there are a number of different approaches to converting sequencing output into micro-RNA counts. Each has their own strengths and biases that impact on the final data that can be obtained from a sequencing run. This
Ernesto, Aparicio-Puerta +3 more
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Massively Parallel Analysis of Regulatory RNA Sequences
2021The stability of RNA transcripts is regulated by signals within their sequences, but the identity of those signals still remain elusive in many biological systems. Recently introduced massively parallel tools for the analysis of regulatory RNA sequences provide the ability to detect functional cis-regulatory sequences of post-transcriptional RNA ...
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Sequence and Structure Analysis of Noncoding RNAs
2009Noncoding RNAs (ncRNAs) are increasingly recognized as important functional molecules in the cell. Here we give a short overview of fundamental computational techniques to analyze ncRNAs that can help us better understand their function. Topics covered include prediction of secondary structure from the primary sequence, prediction of consensus ...
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Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing
Plant Molecular Biology, 1991A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup ...
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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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Vaccinia Virus Transcriptome Analysis by RNA Sequencing
2019RNA-sequencing (RNA-Seq) using next-generation sequencing (NGS) technique is a powerful tool for simultaneous analysis of global transcripts from both vaccinia virus and host cell. Here, we describe an RNA-Seq method for analyzing the vaccinia virus transcriptome from virus-infected HeLa cells.
Shuai, Cao, Yongquan, Lin, Zhilong, Yang
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RNA Sequences Similarities Analysis by Inner Products
2015According to 2-D chaos game representation of RNA secondary structures, we propose a new method of 3-D graphical representation which does not lose any biological information. Then we extract a new numerical feature which called inner products from 3-D graphical representation. It is regarded as a value to analyze the relationship between nine kinds of
Shanshan Xing +3 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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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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