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.
Features
- Very fast tool for scanning entire genome assemblies with a PWM
- Menu-driven selection of common model organism genomes
- Access to large collections of PWMs from MEME and other databases
- Support for custom PWMs
- Support for diverse PWM formats: JASPAR, TRANSFAC, plain text, etc.
- Output provided in various formats: BEDdetail, SGA, FPS, etc
- Direct links to the UCSC genome browser for visualization of results
- Action buttons to transfer match lists to analysis tools (ChIP-Seq Tools, motif analysis)
Project Samples
