Large-scale frequent stem pattern mining in RNA families

DOI10.1016/j.jtbi.2018.07.015zbMath1406.92451OpenAlexW2884687690WikidataQ57467577 ScholiaQ57467577MaRDI QIDQ1714283

Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen, Tharam Singh Dillon

Publication date: 31 January 2019

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

Full work available at URL: https://doi.org/10.1016/j.jtbi.2018.07.015

zbMATH Keywords

topologyRNAsecondary structurebenchmark testingalgorithm design and analysisncRNARNA pseudoknot

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Uses Software

• RNAforester
• Wenxiang
• CMfinder
• iEnhancer-2L
• 2D-MH
• iPro54-PseKNC
• iPhos-PseEvo
• iRNA-AI
• pLoc-mAnimal
• pLoc-mVirus
• pLoc-mEuk
• iRNA-PseColl
• iRNAm5C-PseDNC
• iPreny-PseAAC
• iRSpot-EL
• iPromoter-2L
• pLoc-mGneg
• pLoc-mPlant
• iKcr-PseEns
• Gneg-mPLoc
• iRNA-PseU
• iRNA-3typeA
• pLoc-mHum
• iDNA6mA-PseKNC
• 2L-piRNA
• PROSPERous
• iDNA4mC
• FoldRate

Cites Work

• Unnamed Item
• Some remarks on protein attribute prediction and pseudo amino acid composition
• Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins
• 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids
• The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism
• Support-vector networks
• Forest Alignment with Affine Gaps and Anchors
• A Simple and Faster Branch-and-Bound Algorithm for Finding a Maximum Clique
• Biological Sequence Analysis

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