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Applied and Environmental Microbiology, August 2000, p. 3616-3620, Vol. 66, No. 8
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

Terence L. Marsh,1,2,* Paul Saxman,1 James Cole,1,3 and James Tiedje1,2,3

Center for Microbial Ecology1 and Departments of Microbiology2 and Crop and Soil Science,3 Michigan State University, East Lansing, Michigan 48824

Received 9 February 2000/Accepted 13 May 2000

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 world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-specified primer to the 3' terminus of the restriction endonuclease target site. 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 terminal restriction fragment length polymorphisms.

* Corresponding author. Mailing address: Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824. Phone: (517) 432-1365. Fax: (517) 432-3770. E-mail: MARSHT{at}pilot.msu.edu.

Applied and Environmental Microbiology, August 2000, p. 3616-3620, Vol. 66, No. 8
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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