To install the eMOTIF package, perform the following steps: 1. Obtain the program files in emotif-3.6.tar.gz and the database files in the einputs.tar.gz. Place them in the same directory, and unpack each file: gunzip.gz tar -xvf .tar where corresponds to the appropriate filename. 2. Go into the emotif-3.6 directory. Edit the file site.defs to define various directories and default parameters. Do NOT include any extra spaces around the equals signs. 3. Follow the instructions in the file INSTALL. The directions in that file are the standard installation instructions for the GNU configure package. Program installation requires root privilege. ./configure make make install make check For a customized configuration, the GNU configure package allows you to set certain environment variables, such as CC (your desired C compiler), CXX (your desired C++ compiler), and CFLAGS, before you run configure. The emotif-3.6 package includes a Web interface. This interface will be located in the CGIDIR (currently defined as /home/httpd/cgi-bin) and HTMLDIR (currently defined as /home/httpd/html) directories defined in site.defs. If you do not want to install the Web interface, you may delete these directories after installation. To install the eBAS package, perform the following steps: 1. Put the downloaded file, eBAS-3.6.tar.gz, in the desired location in your filesystem. Type the following two commands: % gunzip eBAS-3.6.tar.gz % tar -xvf eBAS-3.6.tar 2. Once eBAS-3.6.tar.gz has been untarred and unzipped, two files should now exist in the filesystem: % ls eBAS-3.6 eBAS-3.6.tar 3. To configure the eBAS-3.6 automatically for your platform, type the following two commands: % cd eBAS-3.6/ % ./configure ----------------------------------------------------------------------------- To cite this work, use the following reference: Jimmy Y. Huang and Douglas L. Brutlag, "The EMOTIF Database," Nucleic Acids Res., 2001, 29, 202-204. Craig G. Nevill-Manning, Thomas D. Wu, and Douglas L. Brutlag, "Highly specific protein sequence motifs for sequence analysis", Proc. Natl. Acad. Sci., USA, 1998, 95: 5865-5871. Please send questions and comments to ALL of the following people: Jimmy Y. Huang (yhuang@leland.stanford.edu) Thomas D. Wu (twu@gene.COM) Craig Nevill-Manning (http://craig.nevill-manning.com) Douglas L. Brutlag (http://cmgm.stanford.edu/~brutlag)