Perform k-mer abundance analysis in DNA sequences
Project description
eme_selex
eme_selex (Every Motif Ever for SELEX Analysis) is a Python package to perform k-mer abundance analysis in DNA sequences. eme_selex is developed to perform fast and efficient analysis of short k-mers (tested with k-mers up to length 10).
While eme_selex can be used for general purpose k-mer analysis, motivation to develop eme_selex is to perform Systemic Evolution of Ligands by EXponential enrichment coupled with High Throughput sequencing (HT-SELEX) analysis in a Pythonic way. By default, for every k-mer, eme_selex quantifies the fraction of reads containing that k-mer in a non-redundant manner. After the quantification, a basic position frequency matrix (PFM) for the top 50 k-mers is generated. If the user wants to generate more PFMs, they can change the top keyword argument to a desired number.
Installation
pip install eme_selex
Tutorial for HT-SELEX analysis
Jupyter notebooks detailing the usage of eme_selex and extensive analysis for HT-SELEX are hosted here https://eme_selex.readthedocs.io
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