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Updated: Mar 20, 2026

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Published on: January 22, 2018

Intercorrelation of Major DNA/RNA Sequence Descriptors - A Preliminary Study.

Dwaipayan Sen, Subhadeep Dasgupta, Indrajit Pal

¹Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India. anandy43@yahoo.com.

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|May 26, 2016

Summary

This summary is machine-generated.

Graphical representation and numerical characterization (GRANCH) methods for bio-molecular sequences show varying degrees of redundancy. Minimally correlated or principal components (PCs) descriptors are recommended for accurate nucleic acid structure and function analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Numerous alignment-free graphical representation and numerical characterization (GRANCH) methods exist for bio-molecular sequences.
The comparative effectiveness of these GRANCH techniques in assessing sequence similarity and dissimilarity remains largely unquantified.

Purpose of the Study:

To evaluate the relative efficacy of various GRANCH methods for determining similarities and dissimilarities in bio-molecular sequences.
To identify redundant and non-redundant structural information provided by different GRANCH descriptors.

Main Methods:

Selected seven diverse GRANCH methods representing different classes.
Computed sequence descriptors for multiple gene sequence sets.
Performed principal component analysis (PCA) to analyze descriptor variances and correlations.

Main Results:

Identified strong correlations among some descriptors, indicating shared structural information.
Observed distinct separation in other descriptors, suggesting unique information content.
PCA revealed that the first three principal components explain over 97% of the variance in descriptors.

Conclusions:

Some GRANCH descriptors quantify redundant structural information, while others provide non-redundant insights.
Recommends using minimally correlated or orthogonal descriptors, such as PCs, for characterizing nucleic acid structure and function.