----------------------------------------------------------------------------- eMOTIF-3.6 Sequence Analysis Using Pareto-optimal Discrete Motifs March 1, 2002 Jimmy Y. Huang, Thomas D. Wu, Craig G. Nevill-Manning, and Douglas L. Brutlag Stanford University ============================================================================= This package includes the following three programs: (1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family. (2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment. (3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database. ----------------------------------------------------------------------------- QUICK INSTALLATION NOTES To install the program, 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 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)