Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial wor ld and the high complexity of many microbial communities. Several technique s for community analysis have emerged over the past decade, and most take a dvantage of the molecular phylogeny derived from 16S rRNA comparative seque nce analysis. We describe a web-based research tool located at the Ribosoma l Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction f ragment length polymorphism of 16S ribosomal DNA. The analysis function (de signated TAP T-RFLP) permits the user to perform in silico restriction dige stions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-sp ecified primer to the 3' terminus of the restriction endonuclease target si te. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with termin al restriction fragment length polymorphisms.