Bioinformatics Softwares List
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- Category: RNA Analysis (continued)
- LR50 1.0 - Assessing Insect Transcriptomes
- LRIscan - Predict Conserved, Genome-wide Long range RNA-RNA Interactions
- m6Apred - Identification and Analysis of the N6-methyladenosine in Saccharomyces Cerevisiae Transcriptome
- MAGI - Drag-and-drop FASTQ files for microRNA-Seq Analysis
- Magnolia - Classification of Coding and Noncoding RNAs
- Mallard 1.02 - Screen 16S rRNA Clone Libraries contain Chimeras
- MAP-RSeq 1.2.1 - System for RNA-Sequencing Data Analysis
- MapFold - Predicting Secondary Structure of RNA using Chemical and Enzymatic Mapping data
- MapMi 1.5.9 - Automated Mapping of miRNA loci
- MapSplice 2.1.8 - Mapping of RNA-seq reads for Splice Junction Discovery
- MARNA 100729 - Server for Multiple Alignment of RNAs
- MatureBayes - Web-based tool for the Computational Identification of Mature miRNAs
- MaturePred - Identification of microRNAs within novel Plant pre-miRNAs
- MBSTAR - microRNA Binding Site Prediction tool
- mCarts 1.2.0 - Hidden Markov model to predict Clustered RNA Motif sites
- McGenus / TT2NE - Prediction of RNAs Secondary Structures with Pseudoknots
- McQFold - Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling
- mEAT 1.0 - microRNA Enrichment Analysis Tool
- Megraft 1.0.2 - Graft Ribosomal Small Subunit (16S/18S) Fragments onto full-length SSU Sequences
- MEMERIS 1.0 - MEME in Rna's Including Secondary Structures
- meRanTK 1.1.0 - Methylated RNA Analysis ToolKit
- MetaDiff - Differential Expression Analysis on RNA-Seq
- MetalionRNA - Metal Ion Binding Site Predictor
- MetAmp - Meta-amplicon Analysis
- metaRNASeq 1.0.2 - Meta-analysis of RNA-seq data
- Metaxa2 2.1.3 - Identification and Classification of Small Subunit (SSU) rRNA Sequences
- MethyRNA - Identificationof N6-methyladenosine Sites
- microDoR - Prediction of Human miRNA-Mediated Gene Silencing
- MicroLive - Design of live attenuated Virus Vaccine based on microRNA-mediated Gene Silencing
- MicroTar 0.9.6 - microRNA Target Prediction from RNA Duplexes
- MIDP - Identifying microRNAs Associated with Diseases
- MIfold 2 - Predicting RNA Structure using Mutual Information
- miFRame - Analysis and Visualization of miRNA sequencing data in Neurological Disorders
- Migal 2.2 - Compare RNA Secondary Structure
- MIMEAnTo - Profiling functional RNA in Mutational Interference Mapping Experiments
- miMsg - Prediction of miR–mRNA Interaction
- MinoTar - Predict microRNA Targets in Coding Sequence
- MINTbase - Exploration of Mitochondrial and Nuclear tRNA Fragments
- miR_Path - Inferring Cancer-related miRNAs based on Gene Expression data
- miR-AT! 1.6 - Prediction of Combinatorial Activity of microRNAs
- miR-isomiRExp - Analysis of Expression of miRNA at the miRNA/isomiR levels
- miR-PREFeR 0.24 - microRNA PREdiction From small RNA-seq data
- miR2GO - Comparative Functional analysis for microRNAs
- miRA 1.1.1 - micro RNA Identification tool
- MirAlign - MicroRNA Identification Based on Sequence and Structure Alignment
- miRanalyzer 0.3 - microRNA Detection Tool for Next Generation Sequencing Experiments
- miRanda 201008- microRNA Target Detection Software
- MiRAuto 0.011 - microRNA Prediction tool
- miRBoost 1.0 - MicroRNA Precursor Classifier using Boosting SVM
- MiRCat 1.2 - miRNA Sequence Profiling
- MirCheck - Identify Plant miRNA Genes
- miRClassify 1.0 - miRNA Family Classification and Annotation
- miRCluster - Automatically Clustering large-scale miRNA Sequences
- miRComp - Composite MicroRNA Target Prediction
- MirCompare - Algorithm to Compare Plant and Mammalian miRNAs
- miRD - pre-microRNA Detection
- miRDeep-P 1.3 - Analyzing the microRNA Transcriptome in Plants
- miRDeep2 2.0.0.7 / miRDeep* 3.6 - Discovering Known and Novel miRNAs from Deep Sequencing Data
- MiRdup 1.4 - Prediction of the Localization of microRNAs within their pre-miRNA
- MiRduplexSVM - MiRNA-Duplex Prediction and Evaluation Methodology
- miReduce - Correlate the logarithm of Expression Fold Changes
- miREE - miRNA Recognition Elements Ensemble
- MIReNA 2.0 - Find microRNAs with high Accuracy and No Learning
- miRepress - Predict miRNA mediated Target Repression considering both Canonical and noncanonical Binding Sites
- MIReStruC 1.0 - A tool to find microRNA Structural Clusters
- miRExpress 2.1.4 - Analyzing High-throughput Sequencing data for Profiling microRNA Expression
- miRFam 1.0 - Classify miRNA Genes with n-grams and a multiclass SVM
- miRFinder 4.0 - MicroRNA Prediction
- MiRfold 0.2b - Search for a good miRNA-like Folding in Sequence
- MiRGator 3.0 - microRNA portal in Deep Sequencing era
- miRge - Rational and Efficient Approach to miRNA-seq
- miRiam - miRNA Target Prediction
- Mirinho 1.0.0 - Prediction of pre-miRNAs
- miRlastic 1.0 - Integrative Analysis of miRNA and mRNA Expression data
- miRMaid 1.0 - microRNAs data structured for easier access and integration
- miRmap 1.1 / miRmap web - Comprehensive Prediction of microRNA Target Repression Strength
- MirMark - Prediction of microRNA Targets both at Site-level and UTR-level
- MiRmat - Predict mature microRNA from pri-microRNA
- miRMOD 0.3 - miRNA Modification Identification tool
- miRModule - Identification of miRNA modules from high-throughput miRNA-mRNA Binding Experiments
- miRNA Digger - Genome-wide novel miRNA Mining
- MiRNA Profiling 0.2.7 - Profile Content of miRNA Sequencing Run
- miRNA-deKmer - Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy
- miRNA-MATE - A mapping pipeline for SOLiD miRNA data
- miRNACon - Influence of Confounding Factors Age and Sex on microRNA
- mirnaDetect - Predict possible microRNA Precursors within Genome data
- miRNAFold - Ab initio miRNA Precursor Search in Genomes
- miRNAkey 1.2 - Analysis of microRNA Deep Sequencing data
- miRNALasso - microRNA Target Prediction
- miRNAMap 2.0 - Genomic Maps of microRNAs in Metazoan Genomes
- miRNAminer - microRNA Homology Search
- miRNAmRNA 1.0 - miRNA mRNA Expression Integration
- mirnaTA 1.2.3 - miRNA Temporal Analyzer
- MIRO 2.9 - Analyze microRNAs using Next-generation Sequencing Data
- miRPara 6.3 - SVM-based miRNA Prediction tool
- miRPD - miRNA Protein Disease Associations
- MIRPIPE 1.2.1 - miRNA detection and quantification pipeline
- miRPlant v4 - An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data
- MiRPlex 0.1 - microRNA Prediction from High-throughput Sequencing data
- miRpp 1.0 - Plant microRNA Precursor Prediction Tool
- miRpredict - Potential miRNA Identification Tool
- miRPredictor - miRNA Target Predictor based on Support Vector Machine
- mirPRo 1.0.1 - Tool for miRNA-seq Analysis
- miRQuest - Integration of tools on a Web Server for microRNA Research
- miRror 2.0 - A Dual View on Sets of MicroRNAs and their Targets
- MiRScan 3 - Predict microRNA Genes from pairs of Conserved Sequences
- miRSel - Automated Extraction of Associations between microRNAs and Genes from the Biomedical Literature
- miRseqViewer 1.0 - Visualization of Sequence, Structure and Expression for Analysis of microRNA Sequencing data
- mirSOM - microRNA Target Predictions
- Mirsynergy 1.7.0 - Detect Synergistic miRNA Regulatory Modules by Overlapping Neighbourhood Expansion
- miRSystem 20150312 - miRNA integrated System for Target Genes Prediction
- miRTar / miRTarBase 4.5 - Identifying miRNA-target Interactions in Human / microRNA-target Interactions database
- miRTarCLIP 1.0.1 - miRNA-Target Interactions Analysis in CLIP and PAR-CLIP Sequencing Data
- mirTarPri 1.0alpha - miRNA Target Prioritization method
- mirTarVis - Analysis tool for microRNA-mRNA Expression Profile data
- miRtest 1.8 - Combined miRNA- and mRNA-testing
- MiRTif - MicroRNA:Target Interaction Filter
- mirTools 2.0 - non-coding RNA Discovery, Profiling and Functional Annotation based on High-throughput Sequencing
- miRTrail - Analysis of Relationships between miRNAs and mRNAs
- MirtronPred - Intronic miRNAs Predictor
- MIRUMIR - microRNA as Biomarker In Cancer
- miRviewer - Multispecies microRNA Homologous Viewer
- MIRZA - Predicting miRNA-target Site Interactions
- MISIS 2.7 - Mapped short Interfering RNA Spots Identification Software
- MISO 0.5.3 - RNA-Seq Experiments for Identifying Isoform Regulation
- miTEA - miRNA Target Enrichment Analysis
- MiTie - Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples
- miTRATA - microRNA Truncation and Tailing Analysis
- MixMir - Mixed linear models for microRNA Motif Finding
- MMAPPR 0.83 - Mutation Mapping Analysis Pipeline for Pooled RNA-seq
- ModeRNA 1.7.1 - Comparative RNA 3D Modeling
- MPGAfold / MPGAfold Visualizer - Massively Parallel Genetic Algorithm that Predicts RNA Secondary Structure
- MREdictor - MicroRNA Recognition Elements Prediction Tool
- mRNA optimiser 1.0 - Redesign mRNA Sequences to Optimise the Secondary Structure
- mRNAStab - mRNA Stability Analysis
- MSARi - Detecting Conservation of RNA Secondary Structure
- MSbind - Accessibility of microRNA binding sites in meta-stable RNA secondary structures
- MTide - Identification of miRNA-target Interaction in Plants
- multiMiR 1.0.1 - Integration of microRNA-target Interactions along with their Disease and Drug Associations
- MultiMiTar - Predict mRNA Targets of a Given microRNA
- MultiRNAFold 2.0 - Secondary Structure Prediction of RNA/DNA
- MULTo - Identify Unique Resource
- MutualFold - Simultaneous Folding of Alternative RNA Structures with Mutual Constraints
- Myrna 1.2.3 - Cloud-scale Differential Gene Expression for RNA-seq
- nagnag 1.0.3 - Identifyng and Quantifying NAGNAG Alternative Splicing
- NanoStringNorm 1.1.19 - Normalize NanoString miRNA and mRNA Data
- NanoTiler 0.11.1 - Design of RNA Nanostructures
- NASSAM - 3D Pattern Searching in Nucleic Acid Structures
- NASTIseq 1.0 - Detection of Natural Antisense Transcripts using Strand-specific RNA Sequencing data
- ncFANs v2 - non-coding RNA Function Annotation Server
- ncRNAClassifier 1.2 - Identify TE and TE-derived ncRNAs from other ncRNAs
- ncRNAscout - Discovering non-coding RNA in Genome Sequences
- NetUTR 1.0b - Web server for Prediction of Splice Site in 5' UTRs
- NEUMA 1.1.0 - Transcriptome from RNA-Seq data by Effective Length Normalization
- NEXT-RNAi 1.31 - Design and Evaluation of RNAi Sequences on a Genome-wide scale
- nocoRNAc 1.23 - Predict & Characterise ncRNA Transcripts in Bacteria
- Noncoder - Exon Array-based Detection of Long non-coding RNA
- NorahDesk 1.4 - Detecting small non-coding RNA(ncRNA) from Deep Sequencing data (RNA-seq)
- noRNAlize 1.0 - RNA SHAPE Data Normalization software
- Novel miRNA detection 1.0 - Identification of novel miRNA genes
- NOVOMIR 1.11 - de novo Prediction of microRNA-coding Regions in a Single Plant Genome
- novoMiRank - Prioritizing novel predicted miRNA Precursors for Experimental Validation
- Oasis 1.0 - small RNA Classification
- OEFinder 0.0.1 - Identify Ordering Effect Genes in Single Cell RNA-seq data
- OfftargetFinder - web tool for species-specific RNAi Design
- OLego 1.1.6 - Senstive and fast Splice Mapping for mRNA-seq reads
- Oligomap 1.01 - Identification of nearly-perfect matches of small RNAs in Sequence databases
- OligoWalk 2 - Select Efficient siRNA using Hybridization Thermodynamics
- omiRas - Differential Expression Analysis of miRNAs
- OrientationChecker 1.0 - Check Orientation of 16S rRNA Gene Sequences
- ORMAN 1.2 - Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms
- P-SAMS - the Plant Small RNA Maker Suite
- PACCMIT-CDS / PACCMIT - MicroRNA Target Predictions
- pairedBayes 20130514 - Bayesian modeling of paired RNA-seq experiment
- PAL 1.31 - Pseudoknot Aligment for RNA Sequences
- pAliKiss 1.0.7 - Predict Kissing Hairpin Motifs from Aligned Sequences
- PANGEA 1.0.2 - Pipeline Analysis for Next GEneration Amplicons
- PAR-CLIP HMM 0.1.0 - Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP
- ParaRNA 1.0 - Computing Parametric Alignment of Two RNA Structures
- PARma 1.0 - PAR-CLIP data microRNA Assignment
- Parseq rev02 - Infer Transcription level from RNA-Seq Read Counts
- PASPA - mRNA Poly(A) Site predictions in Plants and Algae
- PASTA / PASTA2 - Analysis of RNA-Sequencing data
- PcircRNA_finder - circRNA Prediction in Plants
- PCS 1.5 - Identify and Analyze Conserved K-mers in Pairwise Alignment
- PennSeq - Isoform-specific Gene Expression Quantification in RNA-Seq
- PETfold 2.0 / PETcofold 3.2 - Folding of Multiple Alignment of RNA sequences
- PhaseTank 1.0 - Genome-wide Computational Identification of phasiRNAs
- PHDcleav - Prediction of Human Dicer Cleavage
- PhyloQFold - Bayesian Sampling of Evolutionarily Conserved RNA Secondary Structures with Pseudoknot
- PhyloRNAalifold v1 - Predicting Consensus Structures in RNA Alignments by incorporating RNAalifold with Phylogenetic information
- Piano - Predicting piRNAs
- Pibomd - A web-server Predictor for Identifying piRNAs
- Pintail 1.1 - Analyse 16S rRNA Chimera & Anomalies
- piPipes 1.4.12 - piRNA Pipeline Collection
- PIPmiR 1.1 - Pipeline for the Identification of Plant miRNAs
- piRNA 3.6 / biRNA 3.6 - RNA Interaction Search Engine
- pirnaPre 1.0.0 - piRNA Targets on mRNAs in Mouse
- piRNApredictor 1.0 - Predict piRNA Sequences
- piRPred 1.0 - piwi interacting RNA (piRNA) Prediction
- PITA 6 - microRNA prediction tool
- pKiss 2.2.12 - Folding RNA Secondary Structures
- PKNOTS 1.07 - RNA Pseudoknot Prediction
- PlantMiRNAPred - Classification of Real and Pseudo Plant Pre-miRNAs
- PLATA 1.01 - Probe Level Alternative Transcript Analysis
- PLEK 1.2 - Predictor of Long Non-coding RNAs and mRNAs based on K-mer Scheme
- PLEXY - Target Pprediction for Box C/D snoRNAs
- PLNseq 1.0 - Poisson Lognormal Distribution for High-throughput matched RNA-sequencing Read Count data
- polyester 1.6.0 - Simulate RNA-seq Reads
- POME - Possion Mixed-Effects Regression for RNA-seq Data
- PORTRAIT 1.2 - Prediction of transcriptomic ncRNA by ab initio methods
- PPfold 3.1.1 - Predict Consensus Secondary Structure of RNA Alignments
- PPUS - Predict PUS-specific Pseudouridine sites
- PRADA 1.2 - Pipeline for RNA-Sequencing Data Analysis
- PRI-Modeler 1.3 - Extract RNA Structure elements from PDB files of Protein-RNA Complexes
- Primer - Predicting Protein-binding RNA Nucleotides
- pRNAm-PC - Predicting N6-methyladenosine sites in RNA sequences
- ProbeAlign 0.3 - ncRNA Homology Search
- ProbRNA 20131213 - Modeling RNA Structure Probing data
- PROmiRNA v2 - Annotating miRNA Promoters in Human
- ProMISe 1.8.0 - Infer miRNA-mRNA interactions using paired expression data from a single sample
- PRooF - Detecting Programmed Ribosomal Frameshifting
- PROPER 0.88 - PROspective Power Evaluation for RNAseq
- PseudoViewer 3.0 - Visualization of RNA Pseudoknots of any type
- PSMAlign - Progressive Stem Matching Alignment
- PsRNA - Identification of Putative Small RNA locations within the Intergenic Regions
- psRNATarget - Plant small RNA Target Analysis Server
- psRobot v1.2 - Plant Small RNA Analysis Toolbox
- pssRNAMiner - A Plant short small RNA Regulatory Cascade Analysis Server
- PSTAG 2.1.4a - Model Pseudoknot RNA Structure
- PVAAS 0.1.5 - Identify Variants Associated with Aberrant Splicing from RNA-seq
- pVsupPred 1.0 - Predict Viral Suppressors of RNA Silencing
- QRNA 2.03d - Prototype Noncoding RNA Genefinder
- QRNAseq 0.1.0 - for Functional Isoform, Driver Mutation Gene and Fusion Gene Detection
- QuaCRS 1.2 - Quality Control for RNA-Seq
- Quantas 1.0.8 - Analyze alternative Splicing using RNA-Seq
- r-make 1.0c - Process RNA Sequencing Reads
- R-SAP 1.1 - RNA-Seq Analysis pipeline
- R3D-BLAST - A Search Tool for Similar RNA 3D Substructures
- RACKJ 0.95- Analyze and Compare RNA-seq data made by NGS Technologies
- RactIP 1.2.1 - Joint Secondary Structure Prediction
- RAmiRNA - Viral mature MicroRNA prediction Toolkit
- RandA 1.1.4 - ncRNA Profiling
- Randfold 2.0 - RNA Minimum Free Energy of Folding Randomization Test
- RASER 0.51 - Reads Aligner for SNPs and Editing sites of RNA
- RASP 1.0.1 / WebRASP - Assessing the Stability of RNA Structures
- RASS - RNA Alignment in the Joint Sequence-structure Space
- RBSDesigner 1.0.78 - Design Synthetic Ribosome Binding Sites (RBS) to control Gene Expression levels
- RCARE - RNA-Seq Comparison and Annotation of RNA Editing
- RCAT 3.0 / CATUI 3.51 - RNA Comparative Analysis Tools
- Rcorrector - Error Correction for Illumina RNA-seq Reads
- RCoS - Compute Rank Consistency Score
- Rcount - Simple and Flexible RNA-Seq Read Counting
- RD - Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- rddChecker - software for Detecting RNA-DNA Differences
- RDDpred 1.0 - Random Forest RDD Classifier
- RDiff 0.3 - Accurate Detection of Differential RNA Processing
- RDP Classifier 2.11 - Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
- Read-Split-Walk - Identifying Non-canonical Spliced Regions for RNA-Seq data
- READemption 0.3.7 - A RNA-Seq Analysis Pipeline
- ReadSpy - Assessment of Uniformity in RNA-Seq reads
- REAPR 1.0 - Realignment for Prediction of Structural Non-coding RNA
- RED 0.0.3 - RNA Editing sites Detector
- REDItools 1.0.4 - RNA editing detection by NGS data
- Regliss - RNA Energy Landscape and Saturated Structures
- RegRNA 2.0 - an integrated web server for Identifying Functional RNA Motifs and Sites
- remuRNA - Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation
- repRNA - Web Server for Generating Various Modes of RNA Sequences
- Rfold 0.1.2 - Compute local base pairing Probabilities
- Ribomaker 20140124 - Computational Design of Conformation-based Riboregulation
- riboPicker 0.4.3 - Identification and Removal of rRNA-like Sequences.
- RiboSW - Searching Riboswitches
- Riboswitch finder - Identification of Riboswitch RNAs
- RILogo 1.0 - Visualise RNA-RNA interactions
- RIPSeeker 1.10.0 - de novo RIP Peak Predictions based on HMM.
- RISCbinder - Prediction of Guide Strand of microRNAs
- RIsearch 1.1 - Fast search for RNA-RNA interactions
- RLooM - RNA Loop Modeling
- rlsim 1.4 - Simulating RNA-seq library Preparation with Parameter Estimation
- rMAPS v1.0.1 - RNA Map analysis and Plotting server for alternative Exon Regulation
- rMATS 3.0.9 - replicate Multivariate Analysis of Transcript Splicing
- RME 1.1 - RNA Secondary Structure Prediction incorporating Experimental Constraints
- RMfam 0.3 - Multiple Alignments and Probabilistic Models of RNA Motifs
- RNA - RNA Consensus Secondary Structure Prediction Software
- RNA draw 1.1b2 - RNA Secondary Structure Calculation & Analysis
- RNA FRABASE 2.0 - RNA FRAgment Search Engine $ Database
- RNA Self Containment - Calculates the Self-Containment Index
- RNA-CODE - Noncoding RNA Classification tool
- rna-dm 0.9 - Minimum or Optimal Free Energy Landscape for a RNA sequence
- RNA-DV 1.0 - Design & Visualization Tool for RNA Secondary Structure
- RNA-ensign 0.9.1 - Ensemble-based RNA Secondary Structure Design
- RNA-eXpress 1.4.3 - Extract & Annotate Transcripts from Next Generation RNA sequencing data
- RNA-Pareto 20130814 - Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments
- RNA-Redesign - Web server for Fixed-backbone 3D Design of RNA
- RNA-SeQC 1.1.8 - Quality Control Metrics for RNA-seq data
- RNA-Skim - RNA-Seq Quantification at Transcript Level
- rna-sm beta1 - Mine RNA Structure Elements
- RNA-WL 1.5 - Thermodynamics of RNA structures by Wang-Landau sampling
- RNA22 v2 - microRNA Target Detection
- RNA2DMap v2 - Visual Exploration of RNA Structure
- Rna3Dmotif - Software for Extracting RNA Tertiary Motifs
- RNAalishapes 2.4.7 - Secondary Structure Prediction using Shape Abstraction
- RNAAnalyzer - Identify Regulatory RNA Elements
- RNABOB 2.2 - Fast Pattern Searching for RNA Secondary Structures
- RNAbor - Compute Structural Neighbors of an RNA Secondary Structure
- RNAborMEA - Maximum Expected Accurate Structural Neighbors of an RNA Secondary Structure
- RNAbrowse 1.4 - RNA-Seq de novo Assembly Results Browser
- RNAclust 1.3 - Cluster RNAs based on Secondary Structures
- RNACluster 1.0 - RNA Secondary Structure Comparison and Clustering
- RNAcommender v0.1-beta.1 - Genome-wide Recommendation of RNA-protein Interaction
- RNAComposer 1.0 - RNA Structure Modeling Server
- RNAcon 1.0 - Classification of non-coding RNAs (ncRNA)
- RNAConSLOpt 1.2 - Predicting Consensus stable local optimal Structures for Aligned RNA Sequences
- RNAcontext - Predict the Sequence and Structure Preferences of RNA-binding proteins
- RNAcop 1.0.3 - Optimizing RNA structures by Sequence Extensions
- RNAEAPath 1.0 - Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks
- RNAenn - Energy Parameters and novel algorithms for Extended nearest Neighbor Energy Model of RNA
- RNAentropy 1.0 - Compute RNA Secondary Structure Conformational Entropy
- RNAex - RNA Secondary Structure Prediction Server
- RNAexinv - Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences
- RNAexpNumNbors - Expected Number of Structural Neighbors
- RNAfamily - Java Viewer for RNA Secondary Structures
- RNAfbinv - Fragment-Based Design of RNA sequences
- RNAfdl 1.1.2 - RNA Force Directed Layout
- RNAFold - Create Batch files for the FOLD module of the GCG
- RNAG - Block Gibbs Sampler for RNA Prediction
- RNAgraphdist 1.0 - Calculation of Graph-distance Distribution of the Boltzmann ensemble of RNA Secondary Structures
- RNAHeliCes 2.0.14 - RNA Folding Space Analysis
- RNAhybrid 2.1.2 - Find Minimum Free Energy Hybridisation of RNA
- rnaifold 2.0 - RNA Inverse Folding and Molecular Design
- RNAither 2.18.0 - Statistical analysis of high-throughput RNAi screens
- Rnall 2.0 - RNA Local Secondary Structure Prediction
- RnallViewer 1.0.1 - RNA Analysis Visualization Tool
- RNAlocmin 2.0 - Finds local Minima of RNA + Constructs Barrier Tree
- rnalocopt 20101116 - Compute Partition Function of Locally Optimal RNA Secondary Structures
- RNALogo - Display Structural RNA Alignment
- RNALYZER - RNA Structural Comparison Framework
- RNAmap2D 1.7.5 - Visualization of 2D maps of RNA Structures
- RNAmicro 1.1.3 - Hairpins in a Haystack
- RNAMiner - Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
- RNAML 1.1.2 - Syntax for Exchanging RNA Information
- RnamlView 1.0 - Manipulation, Storage & Visualisation of RNA Data
- RNAmmer 1.2 - Ribosomal RNA Sub Units
- RNAMoIP 1.1 - Insertion of local 3D motifs in RNA Secondary Structures
- RNAMotif 3.1.1 - Find Structural Motifs in RNA
- RNAmotifs 3 - Predict a motif for your own set of RNAs
- RNAMotifScan 5.3 - Automatic Comparing and Searching for RNA Tertiary Motifs
- RNAMotifScanX 0.0.5 - Graph Alignment approach for RNA Structural Motif Identification
- RNAMovies 2.0.4 - Visualization of RNA Secondary Structure
- RNAmutants 2.0 - Analysis of RNA Mutational Landscapes
- RNAMute / XRNAmute - RNA Secondary Structure Mutation Analysis Tool
- rnapagenumber - Compute Optimal "page number" of an RNA Structure
- RNAparametric - Computing the Probability of RNA Hairpin and Multiloop Formation
- RNApasta 1.01 - RNA Structural Alignment & Statistical Analysis
- RNApathfinder - Analyze Near-optimal Folding Pathways between RNA Secondary Structures
- RNApdbee - RNA Secondary Structures Extraction from PDB Files
- RNAplex 0.2 - Search for Short Interactions between two long RNAs
- RNAprofile 2.2 - Secondary structure motif discovery in RNA sequences
- RNApyro - Detect and Correct Pyrosequencing Errors in Noncoding RNAs
- RNArobo 2.1.0 - RNA Structural Motif Search tool
- RNASampler 1.3 - Predict RNA Secondary Structure Motifs
- RNAsc - RNA Secondary Structure Prediction using SHAPE or inline-probing data
- RNAscf 1.1 - Consensus Folding of Unaligned RNA sequences
- RNASeqBias 1.0 - Bias Detection and Correction in RNA-Sequencing Data
- RNASeqBrowser V2 - A Genome Browser for Strand Specific RNAseq Reads
- RNASeqGUI 1.0.0 - GUI for the Identification of Differentially Expressed Genes
- RNASeqMut 0.7 - RNA-Seq Mutation Detection
- RNASeqPowerCalculator - Calculate the Power and Sample size for RNA-Seq Differential Expression
- RNASEQR 1.0.2 - Streamlined and Accurate RNA-seq Sequence Analysis program
- RNASeqR 1.1 - RNAseq Expression Analysis
- RNASeqReadSimulator - A Simple RNA-Seq Read Simulator
- RNAseqViewer 0.8.0 - Visualizing RNA-Seq data
- RNAshapes 3.3.0 - RNA Analysis Package based on Abstract Shapes
- RNAsifter 1.0 - RNA Shape Index Filter
- RNASim 1.0 - RNA Evolution Model
- RNASLOpt - Predicting stable local optimal Structures for RNAs
- RNAsnoop 0.2 - Target Prediction for H/ACA snoRNAs
- RNAsnp 1.1 - Identifying local RNA Structures Disrupted by SNPs
- RNAsoup 1.0a - Structural Clustering Pipeline for Structured RNAs
- RNAspace 1.2 - Platform for Non-protein-coding RNA Annotation
- RNAssess - Quality Assessment of RNA 3D Structures
- RNAstrand 2.0.0 - Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments
- RNAstructure 5.7 - Prediction & Analysis of RNA Secondary Structure
- RNAtips - Analysis of Temperature-induced Changes of RNA Secondary Structure
- RNATOPS 1.2 - RNA Pseudoknot Search in Genomes
- RNAv - Search Genomes for RNA Secondary Structure Variation
- RNAView - Generates 2-dimensional Displays of RNA/DNA Secondary Structures
- RnaViz 2.0.3 - Secondary Structure Drawings of RNA Molecules
- RNAwolf 0.3.2 / MC-Fold-DP - RNA Secondary Structure Prediction.
- RNAxs - Design Potent siRNAs
- RNAz 2.1 - Predict Structural Noncoding RNAs
- RPASuite v0.02 - RNA Processing Analysis Suite
- rpkmforgenes.py - Calculating Gene Expression for RNA-Seq data
- rPredictor - Prediction of Ribosomal RNA Secondary Structure
- rQuant 2.1 - Transcriptome Quantitation from RNA-seq Experiments
- rRNASelector 1.0.1 - Selecting rRNA Genes from Metagenomic and Metatranscriptomic Sequences
- RSEARCH 1.1 - Sequence Database Searching with RNA Structure Queries
- RSEM 1.2.22 - RNA-Seq Expression Estimation by Expectation-Maximization
- rSeq 0.2.1 - RNA-Seq Analyzer
- RSeQC 2.6.2 - RNA-seq Quality Control package
- rSeqDiff 0.1 - Detecting differential Isoform Expression from RNA-seq data
- rSeqNP 1.0 - Detecting Differential Expression and Splicing from RNA-Seq data
- RSEQtools 0.6 - Analyze RNA-Seq data using Compact and Anonymized data summaries
- RSF 0.1.0 - Automated Transcriptome-wide Reconstruction of RNA Secondary Structures
- Rsite - Identify the Functional Sites of Noncoding RNAs
- RSSVM 1.0 - Discover cis-Regulatory RNAs
- RSVP - RNA-seq Variant Prediction
- RVboost 0.1 - RNA-seq Variant Prioritization approach for Illumina Next-generation Sequencing data
- RZParser - Parse Ribose Zipper from PDB file(s)
- S-Mart 1.1.4 - Aid RNA-seq Data Analysis
- Sailfish 0.7.5 - Ultrafast Isoform Abundance Estimation from RNA-seq Reads
- SARA 1.0.7 - Server for Function Annotation of RNA Structures
- SARSE 1.37 - RNA Sequence Editor
- SAVoR - Sequencing Annotation and Visualization of RNA structures
- SbacHTS v5 - Spatial background correction for High-Throughput RNAi Screening
- SCFG Structural Entropy 20120907 - Calculate RNA Structural Entropies through Stochastic Context Free Grammars
- scLVM 0.1 - Modelling framework for Single-cell RNA-seq data
- Scotty - Power Analysis for RNA Seq Experiments
- Sebnif 1.3rc - Comprehensive Novel lincRNA Filter from RNA-seq data
- SECISDesign - Design SECIS-Elements within the Coding Sequence
- SEECER 0.1.3 - SEquencing Error CorrEction for Rna reads
- segmentSeq 2.2.2 - Identifying small RNA loci from High-throughput Sequencing data
- SePIA - RNA Sequence Processing, Integration, and Analysis
- seq2HLA 2.2 - HLA typing from RNA-Seq sequence reads
- SEQBIAS 1.16.0 - Estimation of Per-position Bias in High-throughput Sequencing data
- SeqBuster 3.1 - small RNA analysis of deep Sequencing data
- SeqFold - Genome-scale Reconstruction of RNA Secondary Structure integrating Experimental Measurements
- SeqGSEA 1.9.0 - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
- SeqLogo - Create Sequence Logo from RNA alignment file
- SeqSaw 1.0.8 - Short Spliced Sequence Mapping Tool
- SeqTU r12 - Bacterial RNA-Seq analysis to Identify Transcription Units (TUs)
- Sequgio 0.99.0 - Pre-processing of RNAseq data
- SETTER / MultiSETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm
- SFmap 1.8 - Motifs Analysis and Prediction of Splicing Factors
- Sfold 2.2 - Statistical Folding and Rational Design of Nucleic Acid
- ShortFuse 0.2 - Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs
- shortran 0.43 - A pipeline for small RNA-seq data analysis
- shortran 0.43 - small RNA-seq data analysis
- SI-FI 3.2 - RNAi (RNA interference) Off-target Prediction
- siDirect 2.0 - Target Specific siRNA online Design Site
- SimiRa - Identify Coregulation between microRNAs and RNA-binding proteins
- SimRNA 3.20 - Simulations of RNA Conformational Dynamics
- SimSeq 1.3.0 - Nonparametric Simulation of RNA-Seq Data
- SimTree 1.2.3 - Compute Similarity between RNA Secondary Structure
- siPRED - Predicting siRNA Efficacy using Various Characteristic Methods
- SIREs 2.0 - Iron Responsive Elements Prediction Server
- SMART TOOLS - Implementation of a de novo Genome-wide Computational approach for updating Brachypodium miRNAs
- SMiRK - an Automated Pipeline for miRNA Analysis
- smyRNA 1.2 - Discover Novel ncRNAs in Given Genome
- SNAPR - Scalable Nucleotide Alignment Program RNA-seq
- snoGPS 1.0 - H/ACA snoRNA predictions
- SnoReport 1.2.3 - Computational Identification of snoRNAs with unknown Targets
- Snoscan 1.0 - C/D box snoRNA Predictions
- SnoSeekerNGS - Discovering snoRNAs from pooled Deep-sequencing data
- SnowShoes-FTD - Find Fusions from RNA-Seq data
- SNPfold 1.01 - Identify RiboSNitches by leveraging GWAS data and an Analysis of the mRNA Structural Ensemble
- SNPlice 1.7.2 - Find SNPs influencing splicing in NGS mRNA data
- Solas 0.2.1 - Analysis of RNA-Seq data
- SoMART - Server for plant miRNA/tasiRNA Analysis Tools
- SortMeRNA 2.0 - Filter rRNA Fragments from Metatranscriptomic data
- SoupViewer 0.7.5.2 - Graphical Analysis tool for Output of RNAsoup program
- Spanki 0.5.0 - Analysis of Alternative Splicing from RNA-Seq data
- SPARCS - Structural Profile Assignment of RNA Coding Sequences
- sPARTA 1.12 - small RNA-PARE Target Analyzer
- SPF 1.1 - Find Structurally Significant Regions in RNA Sequences
- SplAdder - Detection and Quantification of Alternative Splicing Events from RNA-Seq data
- SplamiR - Predicting miRNAs in Plants
- SpliceJumper - Splicing Junction Calling from RNA-Seq data
- SpliceMap 3.3.5.2 - Splice Junction Discovery Using RNA-Seq
- SpliceSeq 2.1 - Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data
- SpliceTrap 0.95 - Exon Inclusion Ratio Estimation from Paired End RNAseq data
- SplicingCompass 1.0.1 - Differential Splicing Detection using RNA-Seq data
- SplicingTypesAnno 1.0.2 - Annotation tool for alternative Splicing Types by RNA-Seq data
- SplicingViewer 1.1.0 - Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data
- SPLITS 1.1 / SPLITSX - tRNA Detection in Genome Sequence
- spongeScan - Detecting microRNA Binding Elements in lncRNA Sequences
- SPuNC - RNA Structure Prediction using Nucleotide Composition
- SRAMP - Sequence-based RNA Adenosine Methylation Site Predictor
- srnaloop - Search long DNA/RNA Strings for small RNA Hairpin Loops
- sRNAMap - Small Noncoding RNA MAP
- sRNAscanner 20100831 - intergenic small RNA Detection in Bacterial Genomes
- sRNATarget 2.0 - Prediction of Bacterial sRNA Targets
- sRNATargetNB - Prediction of Bacterial sRNA Targets
- sRNAtoolbox v1.0 - Collection of small RNA Analysis tools
- SSC 0.1 - Sequence Scan for CRISPR
- SSCA - Sequences Selection for the Comparative Approach
- SSCprofiler - miRNA Gene Prediction
- sSeq 1.1 - Detection of Differentially Expressed Genes in RNA-seq Experiments
- SSPcompare - Takes a Library of known RNA Sequence-structure Pairs
- SStructView 1.2.2 - RNA Secondary Structure Viewing Java Applet
- Starfold - Predict RNA Secondary Structures
- sTarPicker - Global Target Prediction for Bacterial small non-coding RNAs
- StarScan 1.2.0 - Scanning small RNA Targets from Degradome Sequencing data
- Stem Kernels 193 - Directed acyclic graph kernels for structural RNA analysis
- StringTie 1.2.2 - Transcript Assembly and Quantification for RNA-Seq
- STRMS 0.5.2 - Structural RNA Motif Search
- Structator 1.1 - Fast Index-based Search for RNA Sequence-structure Patterns
- StructureLab 4.5.0 - RNA Structure Analysis
- SurvMicro v0.9 - Assessment of Prognostic miRNA Signatures
- SVMicrO 20100315 - Mammalian MicroRNA Target Prediction
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