ReadXplorer

ReadXplorer enables comprehensive exploration and analysis of next-generation sequencing (NGS) read mappings to a reference genome or transcriptome, including integrated quality classification of read mappings for genomic and transcriptomic studies.

Key Features:

• Reference Sequence Viewer: Displays base coverage in multiple formats including normalizable plots and histograms.
• Read Alignments and Read Pairs Viewer: Inspects individual read alignments and paired-read relationships mapped to a reference.
• Quality Classification of Read Mappings: Integrates quality classification of read mappings into analyses and visualizations.
• RNA Secondary Structure Prediction: Predicts RNA folding patterns for sequence regions of interest.
• Polymorphism Detection: Identifies single nucleotide polymorphisms (SNPs) and deletion-insertion polymorphisms (DIPs).
• Genomic Feature Analysis: Analyzes genomic elements such as genes, promoters, and other regulatory regions.
• Coverage Analysis: Assesses sequencing depth across datasets and supports combining or superimposing coverage from multiple datasets.
• Differential Gene Expression Analysis: Compares gene expression levels between samples or conditions.
• Transcription Start Site Detection: Detects transcription start sites within mapped datasets.
• Operon Detection: Identifies operons to analyze gene organization in prokaryotes.
• RPKM and Read Count Calculations: Computes RPKM values and raw read counts for expression quantification.

Scientific Applications:

• Mapped-read exploration: Analysis of genomic and transcriptomic NGS reads aligned to a reference genome or transcriptome.
• Variant discovery: Detection and analysis of SNPs and DIPs for genetic variation studies.
• Transcript quantification and comparison: Quantification using RPKM and read counts and comparison via differential gene expression analysis.
• Transcriptional architecture mapping: Identification of transcription start sites and operon structures, including prokaryotic gene organization.
• RNA functional analysis: Examination of RNA secondary structures for functional genomics insights.
• Coverage-based comparative analyses: Comparative assessment of sequencing depth and coverage patterns across multiple datasets.
• Genomic feature and regulatory region analysis: Investigation of genes, promoters, and other regulatory elements in mapped datasets.

Methodology:

Performs quality classification of read mappings; computes and visualizes base coverage as normalizable plots and histograms; inspects read alignments and read pairs; predicts RNA secondary structure; detects SNPs and DIPs; computes coverage metrics and can combine or superimpose coverage from multiple datasets; calculates RPKM values and read counts; performs differential gene expression analysis; detects transcription start sites and operons.