Provides functions to search for any di-nucleotidic Position Weight Matrix (di-PWM) in a genomic sequence (IUPAC compliant).

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  • License: CeCILL-B Free Software License Agreement (CECILL-B) (A package dedicated to search for diPWM motifs in a sequence or a text. Copyright CNRS 2021-; by Mar...)
  • Author: Marie Mille
  • Tags bioinformatics, motif, binding site, transcription, transcription factor, biology, genomics, PWM, Position Weight Matrix, dinucleotide, dinucleotidic, IUPAC
  • Requires: Python >=3.8
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Project description

Package dipwmsearch

Description

This package provides efficient functions to search for one kind of probabilistic motifs known as di-nucleotidic Position Weight Matrices (di-PWMs) in a genomic sequence. The genomic sequence may contain positions with non-ATGC symbols, encoded with IUPAC.

Documentation

A full documentation details how to install and use the package, and also provides ready-to-use scripts for searching a motif in FASTA sequence.

Please refer to: https://rivals.lirmm.net/dipwmsearch/

Contact: dipwm@lirmm.fr

License

License type: CeCILL-B

Authors

  • Marie Mille (main contributor)
  • Bastien Cazaux
  • Julie Ripoll
  • Eric Rivals

Dependencies

Basics to install

For tests

  • pytest
  • pandas

Project details

Verified details  (What is this?)

These details have been verified by PyPI
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Avatar for cazaux from gravatar.com cazaux Avatar for rivals from gravatar.com rivals

Unverified details

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Project links
Meta
  • License: CeCILL-B Free Software License Agreement (CECILL-B) (A package dedicated to search for diPWM motifs in a sequence or a text. Copyright CNRS 2021-; by Mar...)
  • Author: Marie Mille
  • Tags bioinformatics, motif, binding site, transcription, transcription factor, biology, genomics, PWM, Position Weight Matrix, dinucleotide, dinucleotidic, IUPAC
  • Requires: Python >=3.8
Classifiers

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