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

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

Author information

1
Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA.
2
Department of Genetics, Division of Rheumatology, Washington University, St. Louis, MO, USA.

Abstract

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 https://github.com/RobersonLab/motif_scraper.

PMID:
29850891
PMCID:
PMC6223366
[Available on 2019-11-15]
DOI:
10.1093/bioinformatics/bty437

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