dvq 0.0.4.8.3

This is a library to validate and compare dna sequences

DVQ - DNA Visualisations and Quick comparisons

Abstract We introduce DVQ (DNA Visualisations and Quick comparisons), an open-source Python library for exploring nucleotide sequences using a variety of methods. Understanding DNA sequences intuitively is important for a variety of tasks in biology. DVQ aims to be a one-stop comprehensive library that makes explainable DNA easy for geneticists, researchers, and practitioners who need explanations. For practitioners, the library provides an easy-to-use interface to generate visualisations for their sequences by only writing a few lines of code. In this report, we demonstrate several example use cases across different types of sequences as well as visualisations.

Simple early version preprint: http://dx.doi.org/10.13140/RG.2.2.19227.89125

Methods Implemented:

Visual

• Persistant Homological Representations
• ColorSquare
• C-Curve - Removed from development plan due it being redundant vs a 2D Line
• Spider Representation - Removed from development plan due to it being found to be difficult to use for large sequences
• 2D Line
• Chaos Game Representation

Statistical

• Deng entropy
• KL Divergence plain, computes distros of chunks similar to deng entropy.
• KL Divergence KL div like measure using deng entropy.
• KL Divergence
• Perpelxity
• Entropy
• K-Mer overlap
• fast K-Mer overlap, (current implementation is too slow or stuck)
• Wen's Method
• JS Divergence
• Wasserstein Distance

Overview:

• How to use dvq

from dvq import visual

visual.plot_2d_comparison([seqs_1, seqs_2], ['seq_1', 'seq_2'])

from dvq import statistical

statistical.similarity_wen([seqs_1, seqs_2])
# 0.99