Mapping Affymetrix Microarray Probes to the Rat Genome via a Persistent Index

Abstract

A probe mapping technique using a novel implementation of a persistent q-gram index was developed. It guarantees to find all matches that meet certain definitions. These include exact matching of the central 19 bases of 25 base probes, matching the central 19 bases with at most one or three mismatches and exact matching of any 16 bases. In comparison with BLAST and BLAT, the new methods were either significantly faster or identified matches missed by the heuristics. The 16 bp method was used to map the 342,410 perfect match probes from the Affymetrix GeneChip Rat Genome 230 2.0 Array to the genome. When compared with the mapping from Ensembl, the new mapping included over seven million novel matches, providing additional evidence for researchers wishing to further investigate the sources of signals measured in microarray experiments. The results demonstrate the practicality of the index, which could support other q-gram based algorithms.