ModPred - version 1.0 (January 5, 2014) Installation ------------ The ModPred algorithm was implemented and trained in Matlab 2010a. It was subsequently compiled, using different Matlab compilers, into a program that can be run outside of the Matlab environment. In order to run ModPred an appropriate version of the MCRInstaller (we provide Windows and Linux versions) has to be downloaded from http://montana.informatics.indiana.edu/ModPred. Detailed installation instructions generated by the Matlab Compiler are provided below, in the MATLAB Compiler section. Usage Instructions for Windows (64-bit) (in Command Prompt window) ------------------------------------------------------------------ ModPred_win64.exe -i input.fasta -c ptms.config -d pssm_directory -o output.txt -i (Mandatory): input.fasta is a set of sequences of interest, in FASTA format. -c (Optional) : ptms.config is a configuration file that specifies which PTM sites are to be predicted. It is a tab-delimited, 2-column and 23-row file, with the first column containing the names of all PTM types, predictable by ModPred and the second column containing 0s and 1s (Only those PTMs marked with 1s will be predicted). By default, if the configuration file is not provided, sites for all 23 PTM types are predicted (This takes more time). -d (Optional) : pssm_directory is the path to the directory that contains the PSSM files as generated by PSI-BLAST (see the Additional Information section for PSI-BLAST instructions). By default, ModPred uses models without evolutionary features. This directory should be provided if evolutionary features are to be included in the prediction procedure. -o (Optional) : output.txt is a file that will be created by the program. It will contain predictions on all sequences in the input FASTA file. One input/output combination is included (files sample.fasta, sample.config and sample.txt) for testing purposes. Reference ---------- NEED CITATION MATLAB Compiler Instructions for Windows (64-bit) ------------------------------------------------------------ 1. Prerequisites * Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed the specific versions that we have provided (version 8.1 for 64-bit machines). For more information on the MCR Installer, see the MATLAB Compiler documentation. 2. Files to Deploy - ModPred_win64.exe 3. Definitions MCR - MATLAB Compiler uses the MATLAB Compiler Runtime (MCR), which is a standalone set of shared libraries that enable the execution of M-files. The MCR provides complete support for all features of MATLAB without the MATLAB GUI. When you package and distribute an application to users, you include supporting files generated by the builder as well as the MATLAB Compiler Runtime (MCR). If necessary, run MCRInstaller to install the correct version of the MCR. For more information about the MCR, see the MATLAB Compiler documentation. 4. Appendix A. On the target machine, add the MCR directory to the system path specified by the target system's environment variable. i. Locate the name of the environment variable to set, using the table below: Operating System Environment Variable ================ ==================== Windows PATH ii. Set the path by doing one of the following: NOTE: is the directory where MCR is installed on the target machine. On Windows systems: * Add the MCR directory to the environment variable by opening a command prompt and issuing the DOS command: set PATH=\v810\runtime\win64;%PATH% Alternately, for Windows, add the following pathname: \v810\runtime\win64 to the PATH environment variable, by doing the following: 1. Select the My Computer icon on your desktop. 2. Right-click the icon and select Properties from the menu. 3. Select the Advanced tab. 4. Click Environment Variables. NOTE: On Windows, the environment variable syntax utilizes backslashes (\), delimited by semi-colons (;). MATLAB Compiler Instructions for Linux (32-bit and 64-bit) ---------------------------------------------------------- 1. Prerequisites for Deployment * Verify the MATLAB Compiler Runtime (MCR) is installed and ensure that you have installed the specific versions that we have provided (version 7.13). For more information on the MCR Installer, see the MATLAB Compiler documentation. 2. Files to Deploy -ModPred_linux32 -run_ModPred_linux32.sh (shell script run to temporarily set environment variables and execute the application) -to run the shell script, type ./run_ModPred_linux32.sh at Unix or Mac command prompt. is the directory where version 7.13 of MCR is installed or the directory where MATLAB is installed on the machine. is all the arguments you want to pass to your application. For example, If you have version 7.13 of MCR installed in /mathworks/home/application/R2010a/v713, run the shell script as: ./run_ModPred_linux32.sh /mathworks/home/application/R2010a/v713 If you have MATLAB installed in /mathworks/devel/application/matlab, run the shell script as: ./run_ModPred_linux32.sh /mathworks/devel/application/matlab 3. Definitions MCR - MATLAB Compiler uses the MATLAB Compiler Runtime (MCR), which is a standalone set of shared libraries that enable the execution of M-files. The MCR provides complete support for all features of MATLAB without the MATLAB GUI. When you package and distribute an application to users, you include supporting files generated by the builder as well as the MATLAB Compiler Runtime (MCR). If necessary, run MCRInstaller to install version 7.13 of MCR. For more information about the MCR, see the MATLAB Compiler documentation. * NOTE: is the directory where MCR is installed on the target machine. 4. Appendix A. On the target machine, add the MCR directory to the system path specified by the target system's environment variable. i. Locate the name of the environment variable to set, using the table below: Operating System Environment Variable ================ ==================== Linux LD_LIBRARY_PATH ii. Set the path by doing one of the following: NOTE: is the directory where MCR is installed on the target machine. . Add the MCR directory to the environment variable by issuing the following commands: setenv LD_LIBRARY_PATH /v713/runtime/glnx86: /v713/sys/os/glnx86: /v713/sys/java/jre/glnx86/jre/lib/i386/native_threads: /v713/sys/java/jre/glnx86/jre/lib/i386/server: /v713/sys/java/jre/glnx86/jre/lib/i386 setenv XAPPLRESDIR /v713/X11/app-defaults NOTE: To make these changes persistent after logout on UNIX or Mac machines, modify the .cshrc file to include this setenv command. NOTE: on UNIX or Mac, the environment variable syntax utilizes forward slashes (/), delimited by colons (:). NOTE: When deploying standalone applications, it is possible to run the shell script file run_ModPred_linux32.sh on UNIX and Mac instead of setting environment variables. See section 2 "Files to Deploy". 5. For 64-bit systems, the same procedures as above apply, with one exception: All the occurrences of '32' in file/tool names become '64' and 'glnx86' should be replaced with 'glnxa64' Additional Information ---------------------- - IMPORTANT: -> The predictor skips sequences shorter than 30 residues -> All characters other than the standard 20 amino acids (ACDEFGHIKLMNPQRSTVWY) should be removed prior to running ModPred. -> All PSSM files in the directory provided with the '-d' flag should have a .pssm extension and it is recommended that for each multi-FASTA input a separate PSSM directory be created. - STARTUP: -> The first time ModPred is run, it may take up to a few minutes for the program to execute, without anything happening on screen. This is because the MCR takes time to extract relevant files and initialize during the first execution. On a 64-bit Windows machine, with a Core2 Duo processor (3 GHz) and a RAM of 4 GB, startup during the first run takes about 90 seconds. During subsequent runs, this reduces to about 20 seconds. These times will vary depending on the make, usage and age of the computer being used. - PSI-BLAST: -> In order to include evolutionary features, ModPred utilizes position-specific scoring matrices (PSSMs) as generated by PSI-BLAST. -> To do this, it is recommended to use the blastpgp program in the Legacy BLAST package (version 2.2.18) which can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release (This is what was used while training ModPred). -> The nr database was downloaded in June 2013 and a copy is available upon request. -> Command-line parameters for PSI-BLAST: blastpgp -i seq.fasta -d nr -Q seq.pssm -h 0.0001 -j 3 -> For detailed instructions on setting up the nr database, installing & running PSI-BLAST and the relevant file formats, see the PSI-BLAST documentation.