title: Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes.
abstract: BACKGROUND
  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).
  
  
  RESULTS
  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.
  
  
  BACKGROUND
  Available upon request from authors.
authors.affiliation: Department of Computer Sciences, University of Texas at Austin, Austin, TX 78741, USA.
authors.forename: Weijia
authors.initials: W
authors.lastname: Xu
authors.forename: Willard J
authors.initials: WJ
authors.lastname: Briggs
authors.forename: Joanna
authors.initials: J
authors.lastname: Padolina
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Timme
authors.forename: Wenguo
authors.initials: W
authors.lastname: Liu
authors.forename: C Randal
authors.initials: CR
authors.lastname: Linder
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Miranker
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D017931:DNA Primers