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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

wapRNA: a web-based application for the processing of RNA sequences.

Wenming Zhao¹, Wanfei Liu, Dongmei Tian

¹Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China.

Bioinformatics (Oxford, England)

|September 8, 2011

Summary

Researchers developed wapRNA, a comprehensive web tool for analyzing both mRNA and miRNA sequencing data. This tool simplifies gene expression profiling and regulatory mechanism studies for the scientific community.

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

RNA sequencing (RNA-seq) is crucial for profiling gene expression and understanding transcriptional regulation.
Existing RNA-seq analysis tools often lack integrated support for both mRNA and miRNA data.
Accessible web-based tools are needed for the broader RNA-seq user community.

Purpose of the Study:

To develop a comprehensive and user-friendly web application for processing both mRNA-seq and miRNA-seq data.
To provide integrated modules for raw data processing, mapping, gene/miRNA annotation, and functional analysis.
To offer a solution for researchers studying gene expression and regulatory mechanisms.

Main Methods:

Development of the wapRNA web application with distinct modules for mRNA-seq and miRNA-seq analysis.
Integration of data processing steps including read filtering, mapping, and gene annotation or miRNA prediction.
Incorporation of downstream functional analysis tools like Gene Ontology, KEGG pathway analysis, and miRNA target prediction.

Main Results:

wapRNA offers four modules supporting mRNA and miRNA sequencing data from SOLiD or Solexa platforms.
The tool processes raw sequence data, performs mapping and annotation/prediction, and integrates functional analyses.
Executable packages for local server installation are also provided.

Conclusions:

wapRNA serves as a valuable, comprehensive web tool for analyzing both mRNA and miRNA sequencing data.
The application facilitates a deeper understanding of gene expression and transcriptional regulation.
It addresses the need for accessible, integrated RNA-seq analysis solutions for researchers.