New Intraclass Helitrons Classification Using DNA-Image Sequences and Machine Learning Approaches

Wawrzyniak, 2017, The different faces of rolling-circle replication and its multifunctional initiator proteins, Front Microbiol, 8, 2353, 10.3389/fmicb.2017.02353 Kapitonov, 2001, Rolling-circle transposons in eukaryotes, Proc Natl Acad Sci, 98, 8714, 10.1073/pnas.151269298 Kapitonov, 2007, Helitrons on a roll: eukaryotic rolling-circle transposons, Trends Genet, 521, 10.1016/j.tig.2007.08.004 Poulter, 2003, Vertebrate helentrons and other novel Helitrons, Gene, 201, 10.1016/S0378-1119(03)00679-6 Hood, 2005, Repetitive DNA in the automictic fungus Microbotryum violaceum, Genetica, 1, 10.1007/s10709-004-6615-y Pritham, 2007, Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus, Proc Natl Acad Sci, 1895, 10.1073/pnas.0609601104 Thomas, 2015, Helitrons: the eukaryotic rolling-circle transposable elements, Mobile DNA, 3, 893 Platt, 2016, Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome, Mobile DNA, 7, 12, 10.1186/s13100-016-0071-y Thomas, 2014, Rolling-circle transposons catalyze genomic innovation in a mammalian lineage, Genome Biol Evol, 6, 2595, 10.1093/gbe/evu204 Guillen-Ramirez, 2017, Accurate classification of immunomodulatory RNA sequences, 236 Yousef, 2017, Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers, EURASIP J Adv Signal Process, 70, 10.1186/s13634-017-0506-8 Fiannaca, 2015, A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network, Artif Intell Med, 173, 10.1016/j.artmed.2015.06.002 Touati, 2018, A combined support vector machine-FCGS classification based on the wavelet transform for Helitrons recognition in C. elegans, Multimed Tools Appl, 1 Touati, 2019, Distinguishing between intra-genomic helitron families using time-frequency features and random forest approaches, Biomed Signal Process Control, 54, 10.1016/j.bspc.2019.101579 Touati, 2017, SVM Helitrons recognition based on features extracted from the FCGS representation, 1 Touati, 2019, The Helitron family classification using SVM based on Fourier transform features applied on an unbalanced dataset, Med Biol Eng Comput, 1 Almeida, 2001, Analysis of genomic sequences by chaos game representation, Bioinformatics, 429, 10.1093/bioinformatics/17.5.429 Goldman, 1993, Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences, Nucleic Acids Res, 2487, 10.1093/nar/21.10.2487 Jeffrey, 1990, Chaos game representation of gene structure, Nucleic Acids Res, 18, 2163, 10.1093/nar/18.8.2163 Letunic, 2011, Interactive tree of life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Res, W475, 10.1093/nar/gkr201 Vapnik, 1991, Principles of risk minimization for learning theory, NIPS, 831 Vapnik, 2013 Shawe-Taylor, 1998, Structural risk minimization over data-dependent hierarchies, IEEE Trans Inf Theory, 1926, 10.1109/18.705570 Hassan, 2010 Cristianini, 2000 Schiilkopf, 2001, The kernel trick for distances, Adv Neural Inf Process Syst, 13, 301 Hsu, 2002, A comparison of methods for multiclass support vector machines, IEEE Trans Neural Netw, 13, 415, 10.1109/72.991427 Lin, 2003, A study on sigmoid kernels for SVM and the training of non-PSD kernels by SMO type methods, Neural Comput, 3, 1 Szegedy, 2015, Going deeper with convolutions, 1 Haykin, 1994 Breiman, 1999, Random forest, Mach Learn, 45, 1 Yousef, 2018, Species categorization via MicroRNAs-based on 3'UTR target sites using sequence features, Bioinformatics, 112 Kulkarni, 2015, Weighted hybrid decision tree model for random forest classifier, J Inst Civ Eng, 23, 1 Deng, 2013, Gene selection with guided regularized random forest, Pattern Recognit, 46, 3483, 10.1016/j.patcog.2013.05.018 Khaing, 2013, Detection model for Daniel-of-service attacks using random forest and k-nearest neighbors, Int J Adv Res Comput Eng Technol, 2 Efron, 1993, An introduction to the bootstrap, Refrig Air Cond, 57, 436 Pataki, 2008, Classification confidence weighted majority voting using decision tree classifiers, Int J Intell Comput Cybern, 2, 169 Berthold, 2008, KNIME: the Konstanz information mine, 319 Xu, 2001, Monte Carlo cross validation, Chemom Intell Lab Syst, 56, 1, 10.1016/S0169-7439(00)00122-2 “scikit-learn” Çakir, 2010, Systematic computational analysis of potential RNAi regulation in Toxoplasma gondii, 31 Meher, 2016, Identification of species based on DNA barcode using k-mer feature vector and random forest classifier, Gene, 592, 316, 10.1016/j.gene.2016.07.010 Phan, 2017, Combined use of k-mer numerical features and position-specific categorical features in fixed-length DNA sequence classification, J Biomed Sci Eng, 10, 390, 10.4236/jbise.2017.108030 Saitou, 1987, The neighbor-joining method: a new method for reconst ructing phylogenetic trees, Mol Biol Evol, 4, 406 Hammer, 2001, PAST: paleontological statistics software package for education and data analysis, Palaeontol Electronica, 4, 9 Wheeler, 2012, Dfam: a database of repetitive DNA based on profile hidden Markov models, Nucleic Acids Res, 41, D70, 10.1093/nar/gks1265