sibswiss/pwmscan

Sponsored OSS

By SIB Swiss Institute of Bioinformatics

Updated over 2 years ago

A genome-wide Position Weight Matrix (PWM) Scanner

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Data Science
Machine Learning & AI

120

PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site.

PWMScan takes as input a PWM, the background probabilities for the letters of the DNA alphabet, and a threshold score or a p-value. The search is carried out across the entire genome sequence. It can accept PWMs, such as those available in the Transfac or Jaspar databases as well as plain-text PWMs. It computes all occurrences of the PWM in the genome sequence for a given p-value threshold or cut-off. The match list is provided in various genome annotation formats, including BEDdetail, FPS, and SGA.

https://sourceforge.net/projects/pwmscan/

https://gitlab.sib.swiss/EPD/pwmscan

Docker Pull Command

docker pull sibswiss/pwmscan