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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

ReadXplorer--visualization and analysis of mapped sequences.

Rolf Hilker¹, Kai Bernd Stadermann², Daniel Doppmeier¹

¹Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany.

Bioinformatics (Oxford, England)

|May 3, 2014

Summary

This summary is machine-generated.

ReadXplorer is a new software tool that provides comprehensive visualization and analysis for genomic and transcriptomic sequencing data. It uniquely classifies read mappings, aiding in various analyses like gene expression and polymorphism detection.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Genomic and transcriptomic data analysis requires efficient algorithms and visualizations.
Next-generation sequencing data is rapidly increasing in volume.

Purpose of the Study:

To introduce ReadXplorer, a software for analyzing and visualizing genomic and transcriptomic data.
To offer advanced features including read mapping quality classification.

Main Methods:

Developed ReadXplorer as open-source software.
Integrated quality classification into all analysis functions.
Utilized synchronized data viewers for reference sequence, coverage plots, histograms, read alignments, and read pairs.

Main Results:

ReadXplorer provides visualization of reference sequence, base coverage, and read alignments.
It supports RNA secondary structure prediction, SNP/indel detection, and coverage analysis.
For RNA-Seq, it enables differential gene expression analysis, T.S.S. and operon detection, and RPKM/read count calculations.

Conclusions:

ReadXplorer offers a versatile platform for comprehensive genomic and transcriptomic data analysis.
Its unique read mapping quality classification enhances analytical capabilities.
The software facilitates advanced analyses including differential gene expression and polymorphism detection.