Cargando…
AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures
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...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805580/ https://www.ncbi.nlm.nih.gov/pubmed/36440922 http://dx.doi.org/10.1093/bioinformatics/btac752 |
_version_ | 1784862358184656896 |
---|---|
author | Binet, Thomas Avalle, Bérangère Dávila Felipe, Miraine Maffucci, Irene |
author_facet | Binet, Thomas Avalle, Bérangère Dávila Felipe, Miraine Maffucci, Irene |
author_sort | Binet, Thomas |
collection | PubMed |
description | 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-based approach. We showed that AptaMat is able to discriminate between similar sequences, outperforming all the other here considered metrics. In addition, we showed that AptaMat was able to correctly classify 14 RFAM families within a clustering procedure. AVAILABILITY AND IMPLEMENTATION: The python code for AptaMat is available at https://github.com/GEC-git/AptaMat.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9805580 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98055802023-01-03 AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures Binet, Thomas Avalle, Bérangère Dávila Felipe, Miraine Maffucci, Irene Bioinformatics Original Paper 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-based approach. We showed that AptaMat is able to discriminate between similar sequences, outperforming all the other here considered metrics. In addition, we showed that AptaMat was able to correctly classify 14 RFAM families within a clustering procedure. AVAILABILITY AND IMPLEMENTATION: The python code for AptaMat is available at https://github.com/GEC-git/AptaMat.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-11-28 /pmc/articles/PMC9805580/ /pubmed/36440922 http://dx.doi.org/10.1093/bioinformatics/btac752 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Binet, Thomas Avalle, Bérangère Dávila Felipe, Miraine Maffucci, Irene AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title | AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title_full | AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title_fullStr | AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title_full_unstemmed | AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title_short | AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
title_sort | aptamat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805580/ https://www.ncbi.nlm.nih.gov/pubmed/36440922 http://dx.doi.org/10.1093/bioinformatics/btac752 |
work_keys_str_mv | AT binetthomas aptamatamatrixbasedalgorithmtocomparesinglestrandedoligonucleotidessecondarystructures AT avalleberangere aptamatamatrixbasedalgorithmtocomparesinglestrandedoligonucleotidessecondarystructures AT davilafelipemiraine aptamatamatrixbasedalgorithmtocomparesinglestrandedoligonucleotidessecondarystructures AT maffucciirene aptamatamatrixbasedalgorithmtocomparesinglestrandedoligonucleotidessecondarystructures |