Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files

Bioinformatics. 2018 Nov 15;34(22):3926-3928. doi: 10.1093/bioinformatics/bty437.


Summary: Many genomic features are defined not by exact sequence matches, but by degenerate nucleotide motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor motifs, for commonly used model species, identifying the locations of novel motifs, known motifs in non-model genomes, or known motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.

Availability and implementation: The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology
  • Genomics*
  • Nucleotide Motifs*
  • Software*