AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures.

ABSTRACT:

Motivation

Comparing single-stranded nucleic acids (ssNAs) secondary structures is fundamental when investigating their function and evolution and predicting the effect of mutations on their structures. Many comparison metrics exist, although they are either too elaborate or not sensitive enough to distinguish close ssNAs structures.

Results

In this context, we developed AptaMat, a simple and sensitive algorithm for ssNAs secondary structures comparison based on matrices representing the ssNAs secondary structures and a metric built upon the Manhattan distance in the plane. We applied AptaMat to several examples and compared the results to those obtained by the most frequently used metrics, namely the Hamming distance and the RNAdistance, and by a recently developed image-ba

SUBMITTER: Binet T 

PROVIDER: S-EPMC9805580 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature