Using MoBIoS’ Scalable Genome Joins to Find Conserved Primer Pair Candidates Between Two Genomes

For the purpose of identifying evolutionary reticulation events in flowering plants, we determine a large number of paired, conserved DNA oligomers that may be used as primers to amplify orthologous DNA regions using the polymerase-chain reaction (PCR). We develop an initial candidate set by comparing the Arabidopsis and rice genomes using MoBIoS (Molecular Biological Information System). MoBIoS is a metric-space database management system targeting life science data. Through the use of metric-space indexing techniques, two genomes can be compared in O(mlog n), where m and n are the lengths of the genomes, versus O(mn) for BLAST based analysis. The filtering of low complexity regions may also be accomplished by directly assessing the uniqueness of the region. We describe mSQL, a SQL extension being developed for MoBIoS that encapsulates the algorithmic details in a common database programming language, shielding end-users from esoteric programming. Keyword: primer pair, genome comparison, SQL, metric space indexing, biological database