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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

DSAP: deep-sequencing small RNA analysis pipeline.

Po-Jung Huang¹, Yi-Chung Liu, Chi-Ching Lee

¹Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.

Nucleic Acids Research

|May 19, 2010

Summary

This summary is machine-generated.

Deep-sequencing Small RNA Analysis Pipeline (DSAP) offers a comprehensive solution for analyzing small RNA sequencing data. This automated web service facilitates ncRNA and miRNA identification and cross-species comparison.

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AQRNA-seq for Quantifying Small RNAs

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Next-generation sequencing technologies generate vast amounts of small RNA data.
Analyzing this data requires specialized bioinformatics tools for accurate identification and quantification.

Purpose of the Study:

To introduce the Deep-sequencing Small RNA Analysis Pipeline (DSAP), an automated web service for comprehensive small RNA data analysis.
To provide a user-friendly platform for identifying non-coding RNAs (ncRNAs) and microRNAs (miRNAs) from sequencing data.

Main Methods:

DSAP processes tab-delimited input files containing unique sequence reads and their counts.
Analysis involves adaptor and nucleotide trimming, sequence clustering, and homology mapping against Rfam and miRBase databases.
Results are visualized using interactive charts and comparative tools.

Main Results:

DSAP successfully identifies and quantifies ncRNAs and known miRNAs from deep-sequencing small RNA datasets.
Expression levels are presented in user-friendly, clickable multi-color bar charts linked to external databases.
Cross-species comparative analysis of miRNA distribution is enabled.

Conclusions:

DSAP provides an integrated and automated solution for small RNA sequencing data analysis.
The tool facilitates efficient identification, quantification, and comparative analysis of ncRNAs and miRNAs.
DSAP enhances the utility of next-generation sequencing data for small RNA research.