ArticleNucleic acids research2018
BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs.BMC bioinformatics · 2025Article
- Be-dataHIVE: a base editing database.BMC bioinformatics · 2024Article
- Challenges in LncRNA Biology: Views and Opinions.Non-coding RNA · 2024Article
- MFPINC: prediction of plant ncRNAs based on multi-source feature fusion.BMC genomics · 2024Article
- Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches.Current bioinformatics · 2024Article
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- LncRNAs in neuropsychiatric disorders and computational insights for their prediction.Molecular biology reports · 2022Review
- A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs.Nucleic acids research · 2022Article
- PINC: A Tool for Non-Coding RNA Identification in Plants Based on an Automated Machine Learning Framework.International journal of molecular sciences · 2022Article
- Review
- MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors.Briefings in bioinformatics · 2022Article
- Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle.Frontiers in genetics · 2022Article
- Common Features in lncRNA Annotation and Classification: A Survey.Non-coding RNA · 2021Review
- CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts.Briefings in bioinformatics · 2021Article
- LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants.Functional & integrative genomics · 2021Article
- RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction.F1000Research · 2021Article
- Computational Analysis of Transposable Elements and CircRNAs in Plants.Methods in molecular biology (Clifton, N.J.) · 2021Article
- LncMirNet: Predicting LncRNA-miRNA Interaction Based on Deep Learning of Ribonucleic Acid Sequences.Molecules (Basel, Switzerland) · 2020Article
- The computational approaches of lncRNA identification based on coding potential:Computational and structural biotechnology journal · 2020Review
- CircCode: A Powerful Tool for Identifying circRNA Coding Ability.Frontiers in genetics · 2019Article
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5 authors.
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Abstract
With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and non-coding RNAs of 13 species and compared to the CNCI, PLEK and CPC2 methods. BASiNET outperformed all compared methods in all adopted organisms and datasets. BASiNET have classified sequences in all organisms with high accuracy and low standard deviation, showing that the method is robust and non-biased by the organism. The proposed methodology is implemented in open source in R language and freely available for download at https://cran.r-project.org/package=BASiNET.
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