Access the recommendation on F1000Prime
See all news
2018-10-08

New PWMTools Software release

The new software release includes the following updates:
  • New C program pwm_scoring to score FASTA-formatted sequences with either an integer PWM or a base probability matrix;
  • New bash scripts: pwm_scan_ucsc and pwm_mscan_wrapper_ucsc to deal with chromosome files downloaded from UCSC;
  • New bash script pwmlib_scan_seq to scan a sequence with a PWM collection.


PWMTools is a Web interface for Position Weight Matrix (PWM) model generation and evaluation.

PWMs have become a popular method for representing patterns in biological sequences and they are used to extensively study protein-DNA binding specificity, in particular for transcription factor binding site (TFBS) identification.

PWMTools includes the following tools:

  • PWMTrain which is a Web-based software pipeline used to derive TFBS models from DNA sequences such as HT-SELEX and SMiLE-seq
  • PWMEval which is a Web tool to evaluate PWM models based on ChIP-seq data
  • PWMScore which is a Web tool to compute the binding occupancy score of a set of genomic sequences, given a PWM model
  • PWMScan which is a Web tool to scan entire genomes of common model organisms with a PWM


Last update April 2021