PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP‐II database

摘要: We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers use as phylogenetic ecological tools in the identification enumeration of bacteria. PRIMROSE is designed to data from Ribosomal Database Project (RDP) find potentially useful oligonucleotides with up two degenerate positions. The taxonomic range these, other existing oligonucleotides, can then be explored, allowing rapid suitable oligonucleotides. includes features allow user-defined sequence databases used. An silico trial using RDP database identified that described their target taxa degree accuracy far greater than equivalent currently used identify subdivisions Proteobacteria Cytophaga-Flexibacter-Bacteroides (CFB) division. These 94.7% taxon fewer 50 non-target hits, authors recommend they investigated further. A comparison PROBE DESIGN within ARB software package shows capable higher specificity. has an intuitive graphical user interface runs on Microsoft Windows 95/NT/2000 operating systems. It open source freely available authors.