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RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

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Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data.

Jose E Kroll¹, Jihoon Kim², Lucila Ohno-Machado²

¹Institute of Bioinformatics and Biotechnology , Natal, Rio Grande do Norte , Brazil ; Brain Institute, Universidade Federal do Rio Grande do Norte , Natal, Rio Grande do Norte , Brazil.

|December 1, 2015

Summary

This summary is machine-generated.

Splicing Express is a new bioinformatics tool that simplifies the identification and visualization of alternative splicing events (ASEs) from transcriptome sequencing data. This user-friendly software aids researchers in understanding complex biological processes without requiring extensive bioinformatics expertise.

Keywords:

Alternative splicing Bioinformatics Expression Next-generation sequencing RNA-Seq Software Suite tool Transcriptome Visualization

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Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Alternative splicing events (ASEs) are crucial for eukaryotic gene expression and biological function.
Analyzing ASEs is challenging, especially across multiple samples, with existing tools often lacking annotation and visualization.
Next-generation sequencing technologies enable deep transcriptome characterization, necessitating efficient analysis tools.

Purpose of the Study:

To develop a user-friendly software suite, Splicing Express, for the identification and visualization of ASEs.
To provide biomedical researchers, particularly those without bioinformatics backgrounds, with an accessible tool for transcriptome data analysis.
To facilitate the comparison and understanding of ASEs across diverse biological samples and species.

Main Methods:

Splicing Express utilizes a known algorithm for ASE identification, previously implemented in Splooce.
The software performs automatic annotation of transcriptome data using gene coordinates from the UCSC Genome Browser.
It generates HTML files with graphics and tables to visualize ASE expression profiles across samples.

Main Results:

Splicing Express successfully identified known alternative splicing events using RNA-Seq data from the Human Body Map and Rat Body Map.
The software demonstrated a straightforward workflow for analyzing transcriptome sequencing data.
The generated HTML reports provide clear graphical and tabular representations of ASEs.

Conclusions:

Splicing Express offers an efficient and accessible solution for ASE analysis, empowering researchers without specialized bioinformatics skills.
The tool enhances the understanding of biological processes by simplifying the identification and visualization of alternative splicing.
Splicing Express supports data analysis for all species, making it a versatile tool for molecular biology research.