README file for source code of the QUMA 04/17/2008 ABSTRACT: QUMA (QUantification tool for Methylation Analysis) is interactive and easy-to-use web-based tool for bisulfite sequencing analysis of CpG methylation. QUMA includes most of the data-processing functions necessary for the analysis of bisulfite sequences. It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at . COPYRIGHT INFO: The QUMA source code is copyright 2008, Yuichi Kumaki. This is released under the GNU General Public License (GPLv3) These programs are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. These programs are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with these programs. If not, see . PREREQUISITES: The QUMA is written in Perl and can be installed locally. We tested that the QUMA can work at many Linux distributions, Mac OS X and Windows 2000/XP (with cygwin), and will probably work at any UNIX-like OS. (1) Perl open source scripting language You need version 5.6.0 or higher. (2) Web server program The QUMA will probably work with many web server programs which enable to run a perl CGI script. But, we only tested Apache web server program (both version 1.3 and version 2.2). (3) Perl modules Some of these modules may require additional libraries and/or perl modules. (a) CGI::Lite (b) Archive::Zip (c) RTF::Parser (d) GD You need version 2.07 or higher (and libgd version 2.0.12 or higher). (4) needle program of the EMBOSSS software package INSTALLATION: Installation and setting up of the QUMA is not difficult but skill to set up a UNIX/Linux web server is required. Installation to Windows or Mac OS X is more difficult than general Linux distributions, because some additional installations are required to setting up the prerequisites. (1) Change the permission of files/directories in "htdocs" directory as readable from web server program. (2) Change the permission of files/directories in "cgi-bin" directory as executable from web server program. (3) Move all files/directories in "htdocs" directory to web server's DocumentRoot directory. If necessary, change the "index.html" and "index_j.html" to other file name. (4) Move all files in "cgi-bin" directory to web server's cgi-bin directory. (5) Change the setting of the paths of "cgi-bin" directory, needle program and true type font by editing the BFSetting.pm file in "cgi-bin" directory. (a) If necessary, change some other paths at BFSetting.pm file. (b) At UNIX/Linux OS with the X Window System, path of true type font (monospace font is recommended) is usually /usr/X11R6/lib/X11/fonts/TTF/luximr.ttf or /usr/share/X11/fonts/TTF/luximr.ttf or /usr/share/fonts/truetype/freefont/FreeMonoBold.ttf If true type font is not exists in your system, you can download from (6) If necessary, comment out the "AddDefaultCharset" line of the web server's configuration file. Then restart the web server program. WHAT'S NEW: 04/17/2008 1.0.0 First open source version CONTACT: Yuichi Kumaki & Masaki Okano Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan quma@cdb.riken.jp REFERENCE: QUMA: QUantification tool for Methylation Analysis Yuichi Kumaki, Masaaki Oda & Masaki Okano, (2008) Revise Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. Present address for Masaaki Oda: Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK ACKNOWLEDGEMENTS: We thank Akiko Yamagiwa for sample bisulfite sequences of the mouse Gm9 region (1), Morito Sakaue and Masahumi Kawaguchi for constructive feedback on the website, Hazuki S. Hiraga for proofreading of the web site, Yoko Dote for helpful feedback on the "Terms of Use" section, and the Information Networks Office of RIKEN Kobe Institute for helpful suggestions in setting up the Internet connection for the server. This work was supported in part by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan to M. Okano. (1) Oda, M., Yamagiwa, A., Yamamoto, S., Nakayama, T., Tsumura, A., Sasaki, H., Nakao, K., Li, E. and Okano, M. DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner. Genes & Development, 20, 3382-3394 (2006). AUTHOR: Yuichi Kumaki kuma@cdb.riken.jp Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.