eMATRIX, Version 2.0 (March 1, 2002) Sequence analysis using minimal-risk scoring matrices Thomas D. Wu, Craig G. Nevill-Manning, and Douglas L. Brutlag Stanford University ------------------------------------------------------------------------ SUMMARY This package performs the following functions: (1) EMATRIX-SEARCH: EMATRIX-SEARCH determines the function of a sequence. Given a protein sequence, EMATRIX-SEARCH identifies the sequence by finding matches with a precompiled database of scoring matrices. The scoring matrices are generated by the EMATRIX-MAKER program for each alignment block in a given database, such as BLOCKSPLUS. EMATRIX-SEARCH has been optimized for speed, and can be used for genome-wide functional analysis. (2) EMATRIX-MAKER: EMATRIX-MAKER converts an alignment block into a minimal-risk scoring matrix, for use in sequence analysis. EMATRIX-MAKER is used primarily in batch mode to construct the databases for the EMATRIX-SEARCH program. However, the EMATRIX-MAKER program can also be used to convert an individual alignment block into a scoring matrix. That scoring matrix can then be used by EMATRIX-SCAN program to scan a sequence database for homologs. (3) EMATRIX-SCAN: EMATRIX-SCAN searches a sequence database for sequences that match a given scoring matrix. Such a scoring matrix might be generated by EMATRIX-MAKER. For further details for each of these programs, see the man pages in the man subdirectory. -------------------- QUICK INSTALLATION NOTES To install the program, perform the following steps: 0. Obtain the program files in ematrix-.tar.gz and the database files in einputs-blocks.tar.gz and einputs-seqs.tar.gz. Place them in the same directory, and then unpack each file: gunzip .gz tar xvf .tar where corresponds to the appropriate filename. 1. Connect to the ematrix directory. Edit the file site.defs to define various directories and default parameters. Do not include any extra spaces around the equals signs. 2. Follow the instructions in the file INSTALL. These are the standard installation instructions for the GNU configure package. Essentially, you will need to execute the following commands as the root user: ./configure make make install make check For a customized configuration, the GNU configure package allows you to set certain environment variables, such as CC and CFLAGS, before you run configure. The package includes a Web interface. This interface will be located in the CGIDIR and HTMLDIR directories defined in site.defs. If you do not want to install the Web interface, you may delete these directories after installation. If you have any questions or comments, please send e-mail to thomas.wu@stanford.edu.