ArticleBioinformatics (Oxford, England)2023
AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 35 citations in OpenAlex.
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.Molecules (Basel, Switzerland) · 2025Article
- Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools.BMC bioinformatics · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationComparing 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.
resultsIn 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.