xMAN

xMAN maps millions of oligonucleotide fragments to reference genomes by converting sequences to integer hashes and using bit-shifting operations to accelerate alignment.

Key Features:

• Algorithm design: Converts oligonucleotide sequences into integers, hashes them, and stores hashes in RAM to enable bit-shifting operations that speed mapping.
• Speed optimization: Achieves at least one order of magnitude speed increase over existing oligonucleotide mapping tools, demonstrated by mapping 42 million 25-mer probes from Affymetrix whole human genome tiling arrays to a genome in under six CPU hours.
• Enhanced mapping accuracy: Improves mapping accuracy validated by spike-in experiments on ENCODE tiling arrays and estrogen receptor ChIP-chip experiments, with results corroborated by chromatin immunoprecipitation (ChIP) assays and real-time PCR analyses.
• Versatile application: Applicable to diverse high-throughput oligonucleotide mapping needs across genomics, transcriptomics, and epigenetics.

Scientific Applications:

• Genome-wide Association Studies (GWAS): Facilitates mapping of genetic variants across large populations.
• Transcriptomics: Improves alignment of RNA sequencing reads to reference genomes.
• Epigenetic Research: Enhances ChIP-seq and other chromatin profiling techniques through precise probe mapping.

Methodology:

Converts oligonucleotide sequences into integers, hashes them and stores the hashes in RAM, then uses bit-shifting operations to accelerate mapping.