Taiwan Bioinformatics Institute

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Unit 2 : Transcriptomics and metagenomics

Unit2 has established miRTarBase, the most comprehensive miRNA database in the world. Along with miRTarBase,miRNA analytical tools have been made available (miRTar, RNALogo, RNAMST and RegRNA), and related databases have been established, e.g. miRNAMap and Vita.)We have established platforms for miRNA screening and related research to provide customized data analysis services. Our work on circulating miRNA as biomarkers is of high commercial value.

We are also keen in metagenomics, and provide data analysis services in microbiota analysis with the application of NGS technology to explore microbiota so as to address biomarkers for a particular disease or diagnosis. We also provide tools and databases for computer aided drug design, which include the protein structure database related to human genetic disorder, the protein binding site database, the structure-based database of protein-protein interactions and the compound/drug database.

A.On-line services and software

(1) miRTarBase:miRNA-target, database of experimental miRNA-target interaction

(2) miRExpress:NGS for small RNA

(3) miRNAMap: putative microRNA-target interaction database

(4) sRNAMap: sRNA transcription factor targets in microbes

(5) miRStart-Database of microRNA Transcription Start Site

(6) CELLO-Prediction of protein subcellular localization

(7) pKNOT-pKNOT: the protein KNOT web server

(8) (PS)2-Protein Structure Prediction Server

(9) GEMDOCK-Generic Evolutionary Method for molecular DOCKing

(10) SiMMap: Analytical tool for an anchor (pocket-moiety interaction preference) of a site-moiety map

(11) 3D-BLAST-Protein structure search

(12) dbPTM-Protein Post-Translational Modification Database

(13) RegRNA-Regulatory RNA Motifs and Elements Database

(14) RNAMST-RNA Motif Search Tool

(15) SSDB-Disulfide Proteins Database

(16) KinasePhos-Predict phosphorylation sites within given protein sequences

(17) SpliceInfo-An information repository for mRNA alternative splicing in human genome

(18) SDSE-Sequence Derived Structure Entropy

(19) StEQ-Structural Entropy Query

B.Customized services

(1) MicroRNA research:microRNA-target interaction database, miRNA target identification, NGS for small RNA.

(2) Metagenomics data analysis

(3) Structure Bioinformatics: Protein-ligand interaction analysis, Protein structure prediction, Fast protein structure search, Protein-protein interaction (PPI) family, Homologous PPI search, Homologous protein complex search, Homologous MHC-peptide-TCR search

(4) Computer-aided drug design: Lead optimization, New uses for old drugs, Inhibitor identifications, Multiple-target drugs, Binding site identification

(5) Post-translational modification: Protein phosphorylation, glycosylation, methylation, acetylation, and other types of PTM.

(6) Bioinformatics analysis for NGS applications: RNA-seq, ChIP-seq, mRNA-seq, de novo sequencing

(7) Customized Bioinformatics Analysis: Customized integrative analysis for genomics and proteomics data