RNA bioinformatics

DOI10.1007/978-1-4939-2291-8MaRDI QIDQ2259130zbMATH OpenOpenAlexWikidataFDO

Authors

Publication date 27 February 2015

Published in Methods in Molecular Biology (Search for Journal in Brave)

Full work available at URL http://www.springer.com/us/book/9781493922901

zbMATH Keywords

sequence alignmentalternative splicingassemblymiRNARNA secondary structuremultiple alignmentRNA-RNA interactionmotif discovery3D structureRNAseqantagomirartificial RNA moleculeASPicDBAStalavistae-DNA meta-barcodingediting siteExpEditmetatranscriptomemiRNA spongeNGS-Trexpost-transcriptional RNA editingRFAMRIPseq, ViennaRNA web serviceRNA tertiary structureRNAseq workflowUTR regulatory element

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20) Collections of articles of miscellaneous specific interest (00B15) Proceedings, conferences, collections, etc. pertaining to biology (92-06) General biology and biomathematics (92B05) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Recommendations

• RNA sequence, structure, and function: computational and bioinformatic methods
• Bioinformatics and RNA
• Bioinformatics. Volume I. Data, sequence analysis, and evolution
• Bioinformatics. Volume II: structure, function, and applications
• Bioinformatics and the Cell

Cited in

(7)

• RNA sequence, structure, and function: computational and bioinformatic methods
• Regulatory RNAs. Basics, methods and applications
• Bioinformatics for high throughput sequencing
• Deep sequencing data analysis
• MATHT: a web server for comprehensive transcriptome data analysis
• Bioinformatics and RNA
• Computational methods in noncoding RNA research

Describes a project that uses

Uses Software

• R
• STAR
• Bioconductor
• Rfam
• edgeR
• RNAshapes
• onechannelgui
• BaySeq
• ViennaRNA
• EMBOSS
• ClustalW
• Mfold
• KEGG
• Clustal X
• VARNA
• CompaRNA
• Galaxy
• FastQC
• Infernal
• Oases
• SOAPdenovo
• RNAmute
• RNAexinv
• RNAfbinv
• RNAalifold
• CONTRAfold
• Rnaz
• CentroidAlign
• RactIP
• COFOLD
• PicXAA-R
• CENTROIDFOLD
• IPknot
• DAFS
• PETfold
• PETcofold
• PPfold
• RNAG
• R-Coffee
• RNAspa
• RNASTAR
• RNAstructure
• PseudoViewer3
• jViz.Rna
• Assemble
• R-CHIE
• R4RNA
• RILogo
• R2R
• RNA2D3D
• ModeRNA
• RNAplex
• RSeQC
• SeqMap
• SHRiMP
• ASPIC
• PIntron
• Exogean
• REDItools
• NGS-Trex
• SortMeRNA
• ARB
• TagCleaner
• EMIRGE
• Minimus
• TopHat
• RAST
• FragGeneScan
• RSEM
• EBSeq
• RIPSeeker
• PARalyzer
• DARNED
• ExpEdit
• NGS QC Toolkit
• PatSearch
• WAR
• SCOOP
• AstexViewer
• BioMart
• ASPicDB
• PolyA_DB
• BaCelLo
• SPEPlip
• PredGPI
• ASTALAVISTA
• OptiRNAi
• OligoWalk

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