AG Praktische Informatik, University of Bielefeld, 33615 Bielefeld, Germany
ihhermja@techfak.uni-bielefeld.de
The RIFLE system supports a fast method for the 16S rDNA-based identification of microorganisms.
The 16S rDNA is frequently used for the phylogenetic identification of microorganisms [1]. Sequencing large numbers of clones, however, is still costly and time-consuming. The generation of restriction patterns by digestion with restriction enzymes and subsequent fragment length determination is much faster and has been frequently used in taxonomic studies to distinguish species [2].
The RIFLE system compares restriction patterns of possibly unknown microorganisms against a database of theoretical restriction patterns generated from a 16S rDNA database, e.g. the RDP database [3]. It returns a list of microorganisms whose theoretical restriction patterns match the laboratory patterns.
RIFLE has been designed do behave very sensibly in the presence of experimental errors as well as uncertainty in database entries. Restriction patterns of multiple restriction enzymes can be combined to improve the quality of identification, additional parameters allow the individual adaption to laboratory processes, e.g. exactness of fragment length determination.
RIFLE is freely accessible on the WWW.
[1] Amann,R.I., Ludwig,W., Schleifer,K.-H. (1995) Phylogenetic identification
and in situ detection of individual microbial cells without cultivation.
Microbiological Reviews 59:143-169
[2] Gurtler,V., Wilson,V.A., Mayall,B.C. (1991) Classification of medically
important clostridia using restriction endonuclease site differences
of PCR-amplified 16S rDNA. Journal of General Microbiology 137:2673-2679
[3] Maidak,B.L., Olsen,G.J., Larsen,N., Overbeek,R., McCaughey,M.J.,
Woese,C.R. (1996) The ribosomal database project (RDP).
Nucleic Acids Research 24:82-85