XMAN: extreme MApping of OligoNucleotides.

ABSTRACT:

Background

The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies.

Results

We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a genome of any length. By converting oligonucleotides to integers hashed in RAM, xMAN can scan through genomes using bit shifting operation and achieve at least one order of magnitude speed increase over existing tools. xMAN can map the 42 million 25-mer probes on the Affymetrix whole human genome tiling arrays to the entire genome in less than 6 CPU hours.

Conclusions

In addition to the speed advantage, we found the probe mapping of xMAN to substantially

SUBMITTER: Li W 

PROVIDER: S-EPMC2386063 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature