RPISeqclassifiers can reliably predict RNA-protein interactions We compared the performance ofRPISeq-SVMandRPISeq-RFclassifiers to predict RPIs, using the benchmark datasets described above. Table1summarizes the prediction results obtained in 10-fold cross-validation experiments. On the RPI2241 dataset, ...
proteininteractions,theperformanceofRPISeqwascompetitivewiththatofapublishedmethodthat requiresinformationregardingmanydifferentfeatures(e.g.,mRNAhalf-life,GOannotations)oftheputativeRNA andproteinpartners.Inaddition,RPISeqclassifierstrainedusingthePRIDBdatacorrectlypredictedthemajority (57-99%)ofnon-codingRNA-protein...
RPISeq – RNA-Protein Interaction PredictionRPISeq:: DESCRIPTIONRPISeq is a family of classifiers for predicting RNA-protein interactions using only sequence information. Advertisement::DEVELOPERRPISeq team:: SCREENSHOTSN/A:: REQUIREMENTSWeb Browser
Protein-protein interactions We obtain the protein-protein interaction (PPI) data from STRING database V10.045, which contains weighted protein interactions derived from computational prediction methods, high-throughput experiments, and text mining. The confidence scores are computed by combining the probabi...
RPISeq (Muppirala et al., 2011) predicts whether a given pair of protein and RNA interacts with each other. RPISeq cannot be used to find binding regions or sites, but can be used to estimate the interaction probability of a protein–RNA pair. This paper describes a web server called PRI...
Thus, independently of the experiment (PARS, DMS, microarray, X-ray, NMR, eCLIP, PAR-CLIP, HITS-CLIP and iCLIP), the algorithms employed (catRAPID and RPISeq or CROSS to mimic SHAPE data) or organism (PDB database), we found a correlation between number of protein interactions and RNA ...
RNA‒protein interaction prediction. http://pridb.gdcb.iastate.edu/RPISeq/. Accessed 22 Dec 2011. Agnati LF, Fuxe K, Torvinen M, Genedani S, Franco R, Watson S, Nussdorfer GG, Leo G, Guidolin D. New methods to evaluate colocalization of fluorophores in immunocytochemical preparations as...
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. BMC Bioinformatics. 2014;15: 123. doi: 10.1186/1471-2105-15-123.Livi CM, Blanzieri E. 2014. Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and ...
RPISeq 数据库功能: Submit a protein sequence and an RNA sequence to predict the interaction probability. 实例分析:以蛋白AGO2和LncRNA H19为例 Interaction probabilities Prediction using RF classifier 0.55 Prediction using SVM classifier 0.54 两者数值均>0.5,表示预测会相互结合 ...
RPISeq RNA-protein interaction prediction CTF conjoint triad feature SVM support vector machine RF random forest SFPEL-LPI sequence-based feature projection ensemble learning for LPI PseDNC pseudo dinucleotide composition PseAAC pseudo amino acid composition LPI-BLS lncRNA–protein interactions-broad learning...