Predicting DNA binding proteins using support vector machine with hybrid fractal features

DOI10.1016/J.JTBI.2013.10.009MaRDI QIDQ2632482zbMATH OpenOpenAlexWikidataFDO

Authors Xiao-Hui Niu, Xuehai Hu, Feng Shi, Jingbo Xia

Publication date 14 May 2019

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2013.10.009

zbMATH Keywords

cross validationfractal dimensionprotein classificationchaos game representation

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Fractals (28A80) Computational methods for problems pertaining to biology (92-08)

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Cites work

• scientific article; zbMATH DE number 1332320 (Why is no real title available?)
• scientific article; zbMATH DE number 3794378 (Why is no real title available?)
• A classification-based prediction model of messenger RNA polyadenylation sites
• A new hybrid fractal algorithm for predicting thermophilic nucleotide sequences
• Advances in the implementation of the box-counting method of fractal dimension estimation
• Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses
• Fractals related to long DNA sequences and complete genomes
• Knowledge-based computational mutagenesis for predicting the disease potential of human non-synonymous single nucleotide polymorphisms
• Predicting DNA- and RNA-binding proteins from sequences with kernel methods
• Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition
• Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines
• Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation
• Some remarks on protein attribute prediction and pseudo amino acid composition
• Techniques in fractal geometry

Cited in

(5)

• Comparative analysis of bacterial essential and nonessential genes with Hurst exponent based on chaos game representation
• Backbone fractal dimension and fractal hybrid orbital of protein structure
• A new hybrid fractal algorithm for predicting thermophilic nucleotide sequences
• Predicting DNA- and RNA-binding proteins from sequences with kernel methods
• Effective DNA binding protein prediction by using key features via Chou's general PseAAC

Describes a project that uses

Uses Software

• Pfam
• iSNO-PseAAC
• iRSpot-PseDNC
• iDNA-Prot
• GPCR-2L
• BLAST
• PSI-BLAST
• Cd-hit
• AUTO-MUTE

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