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

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