TBI● GMBD Bioinformatics Core for Genomic Medicine and Biotechnology Development I-Shou Chang,Ping-Chiang Lyu, Chao A.Hsiung,Jenn-Kang Hwang,H.Sunny Sun National Health Research Institutes,National Tsing Hua University, National Chiao Tung University,and National Cheng Kung University
GMBD TBI 1 Bioinformatics Core for Genomic Medicine and Biotechnology Development I-Shou Chang, Ping-Chiang Lyu, Chao A. Hsiung, Jenn-Kang Hwang, H. Sunny Sun National Health Research Institutes, National Tsing Hua University, National Chiao Tung University, and National Cheng Kung University
TBI Supporting GMBD GMBD Core NRPGM Infectious Statistical diseases Genetics Services Cancer Computational Collaborative research proteomics Research Comparative Education and Highly heritable Genomics and Training diseases Interactomes Dissemination Structural Innovative Bioinformatics R&D research Applied Medical NRPGM Core Genomics Facilities
GMBD TBI 2 Statistical Genetics Computational proteomics Comparative Genomics and Interactomes Structural Bioinformatics Applied Medical Genomics GMBD Core Services Collaborative Research Education and Training Dissemination R & D Infectious diseases Highly heritable diseases Cancer research Innovative research Supporting NRPGM NRPGM Core Facilities
TBI● GMBD Web portal http://www.tbi.org.tw TI GMBD Bioinformatics Core Bioinformatics Core for Genomic Medicine and Biotechnology Development(GMBD Bioinformatics Core)is a consortium formed by joint efforts of bioinformatics research groups in Taiwan,aiming at becoming bioinformatics infrastructure for our research community Wel ome and enjoy your visit! Unit 1 it 2 Unit 4 Coordination Unit Since 1997.Department of Research Resources at NHRI has de nted considerable amount of resources in providing bioinformatics se ces in Taiwan.Coordination Unit will serve as the administration,education and service center of GMBD Bioinformatics Core. 【ENTER]
GMBD TBI 3 Web portal http://www.tbi.org.tw
TBI GMBD Online Services
GMBD TBI 4 Online Services
TBI GMBD Mirror sites and Databases ■Mirror sites PDB-Protein Data Bank SCOP -Structural Classification of Proteins PredictProtein server-Secondary structure,solvent accessible area prediction ■ln-house Databases SNP-SNP value-added database RegRNA -Regulatory RNA Motifs and Elements Database miRNAMap-Genomic Maps for microRNA CDSPD-CoDing region Sequence and Proteomic Database TAG-Tumor Associated Gene FlyDPI-Drosophila Database of Protein Interactomes hp-DPI-H.pylori Database of protein interactomes GPDB -Genome Profile Database dbPTM-Protein Post-Translational Modification Database Virtual 2D gel-Simulated 2D Gel for complete sequenced microbial genomes IM2PD -Integrated Microbial Metabolic Pathway Database SSDB -Disulfide Proteins Database pKnot-Protein knot structure database
GMBD TBI 5 Mirror sites and Databases ◼ Mirror sites PDB -Protein Data Bank SCOP -Structural Classification of Proteins PredictProtein server –Secondary structure, solvent accessible area prediction ◼ In-house Databases SNP -SNP value-added database RegRNA -Regulatory RNA Motifs and Elements Database miRNAMap - Genomic Maps for microRNA CDSPD -CoDing region Sequence and Proteomic Database TAG-Tumor Associated Gene FlyDPI -Drosophila Database of Protein Interactomes hp-DPI -H. pylori Database of protein interactomes GPDB -Genome Profile Database dbPTM - Protein Post-Translational Modification Database Virtual 2D gel -Simulated 2D Gel for complete sequenced microbial genomes IM2PD -Integrated Microbial Metabolic Pathway Database SSDB -Disulfide Proteins Database pKnot –Protein knot structure database
TBI● GMBD Analysis Tools Homology Similarity BLAST-Basic Local Alignment Search Tool BLAST servers PDB-BLAST -BLAST against PDB protein databank RPS-BLAST -BLAST against Motif/Domain database FASTA-Pair-wise Sequences Alignment ■Sequence Analysis ClustalW-Web-based Multiple Sequence Alignment PDA-Primer Design Assistant RepeatMasker -Screening for low complexity DNA sequences [mirror GPRM-Genetic Programming for RNA Motifs GenePredict -Web-based gene prediction service KinasePhos -Predict phosphorylation sites within given protein sequences Splicelnfo -An information repository for mRNA alternative splicing ProSplicer-An Alternative Splicing Database based on Protein,mRNA,and EST Sequences MuSiC -Multiple Sequence Alignment with Constraints GPRM Genetic Programming for RNA Motifs RNAMST -An efficient and flexible search tool for RNA structural homologs CELLO -Prediction of protein subcellular localization 6
GMBD TBI 6 Analysis Tools ◼ Homology & Similarity BLAST -Basic Local Alignment Search Tool BLAST servers PDB-BLAST -BLAST against PDB protein databank RPS-BLAST -BLAST against Motif/Domain database FASTA -Pair-wise Sequences Alignment ◼ Sequence Analysis ClustalW -Web-based Multiple Sequence Alignment PDA -Primer Design Assistant RepeatMasker -Screening for low complexity DNA sequences [mirror ] GPRM - Genetic Programming for RNA Motifs GenePredict -Web-based gene prediction service KinasePhos -Predict phosphorylation sites within given protein sequences SpliceInfo -An information repository for mRNA alternative splicing ProSplicer -An Alternative Splicing Database based on Protein, mRNA, and EST Sequences MuSiC -Multiple Sequence Alignment with Constraints GPRM Genetic Programming for RNA Motifs RNAMST -An efficient and flexible search tool for RNA structural homologs CELLO -Prediction of protein subcellular localization
TBI● GMBD Analysis Tools RegRNA A Regulatory RNA Motifs and Elements Finder ESTviewer A Web interface for visualizing ESTs 黑器 AComparative Method for Identification of Gene Structures and Alteratively ENACE System Identification and evolutionary analysis of novel exons and alternative splicing events Phylogenetic Analysis POWER-Phylogenetic Web Repeater ■Proteomics KPST-Pathway search tool for KEGG RMA -A Reinforced Merging methodology for mapping unique peptide Tm Predictor -Melting Temperature Prediction:Predict thermal stability of proteins ■Structural Analysis SARST-Structure Alignment by Ramachandran Search Tool StEQ-Structural Entropy Query SDSE-Sequence Derived Structure Entropy PS)2-Protein Structure Prediction Server GEMDOCK -Generic Evolutionary Method for molecular DOCKing ProKware-A graphic web server for presenting protein structural properties
GMBD TBI 7 Analysis Tools RegRNA A Regulatory RNA Motifs and Elements Finder ESTviewer A Web interface for visualizing ESTs PSEP System A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants ENACE System Identification and evolutionary analysis of novel exons and alternative splicing events ◼ Phylogenetic Analysis POWER -Phylogenetic Web Repeater ◼ Proteomics KPST -Pathway search tool for KEGG RMA - A Reinforced Merging methodology for mapping unique peptide Tm Predictor - Melting Temperature Prediction : Predict thermal stability of proteins ◼ Structural Analysis SARST -Structure Alignment by Ramachandran Search Tool StEQ - Structural Entropy Query SDSE - Sequence Derived Structure Entropy (PS)2 -Protein Structure Prediction Server GEMDOCK -Generic Evolutionary Method for molecular DOCKing ProKware -A graphic web server for presenting protein structural properties GMBD
TBI GMBD Analysis Tools ■Miscellaneous Tools -GCG-Wisconsin Sequence Analysis Package Seq Web -Web-based GCG EMBOSS -European Molecular Biology Open Software Suite JEMBOSS -Java user interface of EMBOSS EMBOSS GUI-Web-based service of EMBOSS
GMBD TBI 8 Analysis Tools ◼ Miscellaneous Tools － GCG -Wisconsin Sequence Analysis Package － SeqWeb -Web-based GCG － EMBOSS -European Molecular Biology Open Software Suite － JEMBOSS -Java user interface of EMBOSS － EMBOSS GUI -Web-based service of EMBOSS
TBI● GMBD Software Incorporating endophenotypes in linkage analysis Break point search based on array-CGH data Segregation analysis based on onset time Time course transcription profile of virus genome 9
GMBD TBI 9 Software ◼ Incorporating endophenotypes in linkage analysis ◼ Break point search based on array-CGH data ◼ Segregation analysis based on onset time ◼ Time course transcription profile of virus genome
TBI● GMBD Usage of hp-DPI:H.pylori Database of protein interactomes 8000 7000 6608 口Accumulative Visits 5807 6000 5000- Visits 4000 3402355 3000 2730 2162 2000 1549 1178 1000 630 279 02 2004/Q4 2005/Q2 2005/Q4 2006/Q2 2006/Q4 20071Q2 20071Q4 Accumulative visits of hp-DPI,Nov.2004 to Nov.2007 10
GMBD TBI Accumulative visits of hp-DPI, Nov. 2004 to Nov. 2007 10 Usage of hp-DPI : H. pylori Database of protein interactomes