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

Introduction

In this paper two things are addressed. The first is the provision of a novel implementation of a persistent q-gram index using a relational database management system (RDBMS). This implementation allows a greater value of q than has previously been reported. Further, it demonstrates the use of the RDBMS as a means of accessing the information stored on disk, the traditional bottleneck in the use of persistent indices.

Secondly, the index is applied to the task of mapping Affymetrix microarray probes, thereby demonstrating the practical use of the index implementation and providing a data set of use to those using the RAE 230 microarray. The advantage of our mapping approach is that it provides computational guarantees about the returned matches, making it possible to be certain that all matches meeting the chosen definition have been returned. Further, it is demonstrated that this can be achieved in reasonable time. The problems with the mappings provided by Affymetrix and the benefits of re-mapping are described below.