Building phylogenetic trees from binary oligonucleotide fingerprint vectors

Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) is a method that permits the identification of microorganisms through ribosomal RNA gene (rDNA) analysis. OFRG sorts arrayed rDNA gene clones into clusters through a series of hybridization experiments, each using a single oligonucleotide probe. This series of hybridization experiments generates a "fingerprint" for each rDNA done. The fingerprints are binary vectors that specify whether the probes hybridized or did not hybridize to the clones. Identification of the microorganisms is accomplished by clustering fingerprints from unidentified clones with those from identified clones. The most accurate taxonomic classifications from rDNA analysis are often obtained through complete nucleotide sequence analysis. However, the direct information that we acquire from OFRG is the presence or absence of a specific substring of nucleotides in the unidentified rDNA sequence. This paper provides several ways to associate information to the set of fingerprints obtained by OFRG.