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Bioinformatics Advance Access published online on May 18, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl186
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 6, 2006
Revised April 25, 2006
Accepted May 10, 2006

Applications note

TRFMA: a Web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight

Yoshio Nakano 1 *, Toru Takeshita 1, and Yoshihisa Yamashita 1

1 Department of Preventive Dentistry, Faculty of Dental Science, Kyushu University, Fukuoka-shi, Japan

* To whom correspondence should be addressed.
Yoshio Nakano, E-mail: yosh{at}dent.kyushu-u.ac.jp


  Abstract

Summary: TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50,000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser.

Availability: TRFMA is freely available at http://myamagu.dent.kyushu-u.ac.jp/bioinformatics/trfma/index.html and can be downloaded at at the same site.

Associate Editor: Joaquin Dopazo
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