abc4pwm

abc4pwm is a tool to cluster and classify transcription factors. The abc4pwm algorithm uses Position Weight Matrices (PWMs) optionally with knowledge of DNA-Binding Domains.

Topic

Transcription factor binding site prediction

Detail

  • Operation: Classification

  • Software interface: Command-line user interface

  • Language: Python

  • License: The MIT licence

  • Cost: Free

  • Version name: 0.1

  • Credit: The South-Eastern Norway Regional Health Authority (HSØ 2017061 and HSØ 2018107), Radiumhospitalets Legater, the Norwegian Research Council NOTUR project, FRIPRO project , National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: Junbai Wang: junbai.wang@medisin.uio.no, omerali.0191@gmail.com

  • Collection: -

  • Maturity: Emerging

Publications

  • abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis
  • Ali O, Farooq A, Yang M, Jin VX, Bjørås M, Wang J. abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. BMC Bioinformatics. 2022 Mar 3;23(1):83.
  • https://doi.org/10.1186/s12859-022-04615-z
  • PMID: 35240993
  • PMC: -

Download and documentation

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