"pwm_predict" is the standalone version of PWM predictor

You can download the standalone program allowing predicting Position Weight Matrices for multiple proteins. Current version is available for Windows and Linux. The pwm_predict is a binary executable program for the active platform (Windows or Linux). You can install the program simply by unzipping it. You can run the program by opening the folder and launching the pwm_predict executable inside it.

To predict PWMs for the proteins of your interest, you have to put all their sequences into a single FASTA file. The program will search for C2H2-ZF domains in every sequence and analyze the size of the linkers connecting adjacent domains. Two C2H2-ZF domains are considered to belong to the same DNA-binding array if connected by a linker shorter or equal to the maximum size chosen (default value is 10 amino acids). You can also choose the prediction method, as well as some parameters for SVM predictor (for full list of options please type "pwm_predict --help".

Download pwm_predict 1.0 beta (2015-09-29):

Link Type Size Description
Download .zip 10MB pwm_predict for 32/64-bit Windows
Download .tar.gz 18MB pwm_predict for Linux (x86 binaries)