PerM

PerM maps short reads to large reference genomes using periodic spaced seeds to increase mapping sensitivity and speed for next-generation sequencing data such as ABI's SOLiD and Solexa.

Key Features:

• Efficient Data Indexing: PerM employs a compact index that requires only 4.5 bytes per base for the human genome, allowing the entire genome to be loaded into memory for rapid access.
• Periodic Spaced Seeds with Weight Maximization: PerM uses weight-maximized periodic spaced seeds that provide full sensitivity for up to three mismatches and high sensitivity for four and five mismatches.
• Parallel Processing Capability: PerM is optimized for multi-processor environments to perform simultaneous mapping of reads to the reference genome and reduce computational time.
• Minimization of Random Hits: PerM minimizes random hits per query to accelerate running time while maintaining mapping accuracy.
• Platform Suitability: PerM is tailored to handle high-throughput data from ABI's SOLiD (color-space) and Solexa sequencing platforms.

Scientific Applications:

• Whole-genome sequencing mapping: Mapping reads in whole-genome sequencing projects and large reference genomes such as the human genome.
• Next-generation sequencing data processing: Accurate alignment of reads produced by ABI's SOLiD (color-space) and Solexa technologies.
• High-throughput read alignment: Processing large sequencing datasets to improve speed and sensitivity in genomic research.

Methodology:

PerM builds a compact index (4.5 bytes per base), applies weight-maximized periodic spaced seeds for read mapping with full sensitivity up to three mismatches and high sensitivity for four and five mismatches, executes parallel multi-processor mapping, and implements strategies to minimize random hits per query.