PET-Tool

PET-Tool processes and maps Paired-End diTag (PET) sequencing data to reference genomes to enable transcriptome and genome characterization in mammalian studies.

Key Features:

• Integrated Computation Program Package: Automates the workflow from raw PET reads through extraction, quality assessment, artifact removal, and genomic mapping within a cohesive software suite.
• Modular Design: Implements separate modules to stage processing and analysis for PET datasets.
• Extractor Module: Extracts PET sequences from raw sequencing data, selecting relevant and high-quality PET tags for downstream analysis.
• Examiner Module: Performs analytic quality assessment and identifies or removes artifacts to improve PET data integrity.
• Mapper Module: Maps high-quality PET sequences to reference genome sequences using optimized criteria, achieving over 70% specific mapping efficiency.
• ProjectManager Module: Organizes multi-layered PET datasets to support integration with downstream bioinformatics analyses.
• Performance and Efficiency: Validated on a dataset of 2.7 million PET sequences, demonstrating high accuracy in sequence extraction and artifact removal and processing approximately one million PETs from extraction to mapping within six hours on a 2.4 GHz LINUX machine.

Scientific Applications:

• Transcriptome Characterization: Enables transcriptome profiling and boundary resolution using PET-derived tag pairs.
• Gene Expression Profiling: Supports quantitative analysis of gene expression from PET data in mammalian studies.
• Structural Variant Detection and Genome Characterization: Facilitates precise sequence mapping for detection of structural variants and other genome-level analyses.

Methodology:

Automated extraction of PET sequences from raw reads, analytic quality assessment and artifact removal, followed by mapping of high-quality PETs to reference genomes.