Home
Category
Visualization
BarBoxComutationDotForestHeatmapHistogramLollipopMafsummaryMaftitvManhattanOncoprintPM-AdiversityPM-comp-corPM-comp-funcPM-comp-taxaPM-DistributionPM-HclusterPM-HeatmapPM-Marker-CorrPM-Marker-RFscorePM-Marker-TestPM-NetworkPM-PcaPM-PcoaPM-plot-taxaQ-QSurvivalUpsetVenn
Sequence alignment
BLASTDotmatcherDotpathDottupNeedlePM-BdiversityPM-extract-rnaPM-parallel-metaPolydotWater
RNA Expression
Bulk RNA-seq Data AnalysisCancer Alternative Splicing AnalysisCCLHunterCIRI-deepCIRI3Cross-disease analysisDisease predictionEditing site annotationEditing site identificationEditingFactorDetectorFunGenGene-disease network constructionNCSelPredRNA-seq AnalysisSingle-cell RNA-seq Data AnalysisSPIRALTIVar diffTIVar predictVisualization of scRNA-seq Data Analysis Results
Variome analysis
BarcodeBLASTBarcodeFindereasyGWASExpPatternGeneFinderHaplotype analysisHapMapHapSnapLeadSNPFinderRice Varieties IdentificationRice Yield EstimationSeqFetchVersionMapWheat Head Estimation
Epigenome analysis
Age PredictorBS-RNAComparative analysis in nucleosomesDMR AnnotationDMR ToolkitEnrichment & AnnotationEnrichment analysis in nucleosome occupancyEWAS Network VisualizationGMQNIDMPLollipop PlotterMRAS
Long non-coding RNA
ClassificationFunctional PredictionID conversionLGClncbook-BLASTLncBot
Virus
COVID-19 genome variation annotationCOVID-19 haplotype analysisDenovo AssemblyEvolutionary treeFastq-to-VariantsGenealogy and Evolutionary AnalysisGenome AnnotationGenome TracingMcANMonkeypox virus genome variation annotationMonkeypox virus genome variation identificationPangolin COVID-19 Lineage AssignerSeqQCVENASVISTA
Single-cell omics
BroCOLICell Type ComparatorCell Type PredictorFGOTGOTSCSESSpaMITACOSUCASpatial
Image Processing
Image CroppingImage DenoisingImage FlippingImage PartitioningImage Resizing
Others
APAcatcherComposition analysisCross-model analysisCross-species analysisCross-stages analysisHomolog FinderLUTLSRSMIAncRNA-eQTLPM-predict-func
User Manual
RNA Expression
Bulk RNA-seq Data AnalysisCancer Alternative Splicing AnalysisCCLHunterCIRI-deepCIRI3Cross-disease analysisDisease predictionEditing site annotationEditing site identificationEditingFactorDetectorFunGenGene-disease network constructionNCSelPredRNA-seq AnalysisSingle-cell RNA-seq Data AnalysisSPIRALTIVar diffTIVar predictVisualization of scRNA-seq Data Analysis Results
Home RNA Expression
TIVar diff
File Type
tivarDiff
tivarDiff

Data

input variants (vcf)
Example file
gene annotation (bed)
Example file

Parameters

References
https://github.com/zhpn1024/TIVar
Instructions

Prediction of translation initiation efficiency and changes by SNP/Indel variation.

Predict RNA translation initiation TI efficiency for potential start codons, based on the context sequence near the start codon. Given SNP/Indel variation, this tools can predict changes of TI efficiencies between ref and alt alleles.

Contributor(s)
Peng Zhang
zhangp@ibp.ac.cn
#Runs
5
Open Result
SeqID Pos StartSeq EffScore s1 36 GACGTGTTA-ATG-GGGC 0.16086 s1 51 CCCAGACCT-ATG-GATT 0.2331 s1 113 AGAGCCAAG-ATC-TGCC 0.05275 s1 125 TGCCCAGGA-CTG-GAAT 0.05669 s1 130 AGGACTGGA-ATG-CTTT 0.05996 s1 194 GTACAATTC-ATG-TGCT 0.06007 s1 212 TGGGTTTGG-ATG-GCAC 0.13032 s1 259 GGCACCAAC-ATT-AACC 0.08637 s1 266 ACATTAACC-CTG-ACAG 0.09722 s1 295 TTCCAGGAA-CTG-GAAG 0.07995 s1 331 GAGGTCATC-ATG-ATCA 0.32589 s1 386 CTGAGAGCT-ATG-AGGC 0.21162