cbgr/jaspar_matrixaligner repository overview

⁠JASPAR Matrix Aligner

The JASPAR Matrix Aligner Tool aligns an input DNA binding motif (PFM matrix, JASPAR string, or IUPAC sequence) against motifs retrieved from the JASPAR database. It utilizes the C++ matrix_aligner JASPAR tool to compute optimal alignment scores, strand orientations, and offsets, generating both a CSV summary report and aligned SVG sequence logos.

It can be used as a Pixi package or as a Docker image.

The source code can be foud on Bitbucket⁠.

⁠Quick Start

# 1. Pull the Docker image
docker pull cbgr/jaspar_matrixaligner

# 2. Run the container
docker run -it \
   -v $(pwd)/my_file.txt:/app/my_file.txt \
   -v $(pwd)/output:/app/output \
   cbgr/jaspar_matrixaligner -f my_file.txt -t jaspar -c CORE -g vertebrates