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Taiwan Bioinformatics Institute

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Nucleotide Databases
GBRED (Gene-Based Repetitive Element Database) is a dedicated database containing repetitive element information which focus on the sequences flanking all human genes, such as 5' untranslated region (5'UTR), and 3' untranslated region (3'UTR). [NCKU]  
A database of copy number variations across vertebrate genomes. [Sinica, NHRI]
CNVVdb is a web interface for identification of potential inter-species CNV information by finding duplicated regions within a genome (paralogues) and between different genomes (orthologues).		  
Genome Profile Database [NTHU]
GPDB has been developed to provide and compare features of the fully sequenced organisms in a graphic and easy-reading way. We provide some "Genome Profile", develop on-line graphic browsing interface and use hierarchical clustering method to compare and view the difference between these organisms.		  
Genomic Maps for microRNA [NCTU]
MicroRNAs (miRNAs) are small noncoding RNA molecules, which are capable of negatively regulating gene expression to control many cellular mechanisms. In this work, we develop a resource, miRNAMap 2.0, to collect experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. 		Manual

Database of microRNA Transcription Start Site [NCTU]
miRStart, a novel resource of human microRNA TSSs (transcription start sites), systematically incorporates significant datasets derived from TSS-relevant experiments to identify transcription start sites of microRNAs. The distribution patterns of these experimental features within 50 k upstream region of microRNA precursors provides an insight into determining reliable microRNA TSSs. In general, a high-confidence TSS is recommended for each microRNA based on a SVM training model. However, users can customize their preferable microRNA TSSs according to the straightforward display of experimental TSS signals.

 

miRNA-target Interactions Database [NCTU]
miRTarBase has accumulated more than three thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

Manual
Regulatory RNA Motifs and Elements Database [NCTU]
RegRNA is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.		 Manual
Screening for low complexity DNA sequences and interspersed repeats [mirror at NCKU]
RepeatMasker is a program that screens DNA sequences for low complexity DNA sequences and interspersed repeats. The masked out sequence can be used for example BLAST searches. Repeats are stored in the database		 Manual

Tumor Associated Gene [NCKU]
The tumor-associated gene (TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed database.

  
The Binding Element Searching Tool [NCKU]
The Binding Element Searching Tool is an online genome-wide searching tool. Users can build up a customized hidden markov model (HMM) via HMMER program by upload or paste a set of element sequences containing specific transcription factor binding site (in FASTA format) and use this model to search the multi-species promoter region (human, mouse and rat) retrieved from the EnsMart system annotated by ensembl project.		 Manual
Taiwan Polymorphism Marker Database [NHRI]
TPMD contains microsatellite markers with di-, tri-, and tetranucleotide repeats deposited by four qualified genotyping laboratories and presented with user-friendly web interfaces for researchers. 		Manual
SNP SNP -SNP value-added database [NCKU]
The value-added SNP database was designed to fulfill this need by incorporation of SNP data from dbSNP and HGVbase with SNP data established in Chinese population. The user friendly web interface provides two conventional ways to browse information collected in the database.
CircNet Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression [NCTU]
We constructed the CircNet database that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms.
     
Protein Databases
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Comparative Analysis of Protein Interactions for HIV-1 [NHRI]
CAPIH aims to provide HIV and AIDS researchers a comparative view of host-HIV-1 protein interactions between human and three major animal models: chimpanzee, rhesus macaque, and mouse. The interface demonstrates that a considerable number of differences exist between human and the model organisms, including amino acid substitutions, insertions/deletions, and post-translational modifications (PTMs). 		Manual
Protein Post-Translational Modification Database [NCTU]
dbPTM was proposed to integrate experimentally verified PTMs from several databases, and to annotate the predicted PTMs on Swiss-Prot proteins. This update extends dbPTM to a knowledgebase comprisingthe modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains and protein variations. 		Manual
Drosophila Database of Protein Interactomes [NHRI]
Fly-DPI is the online database and an integrated proteomics tool with comprehensive protein annotation information from major databases as well as an effective means of predicting protein-protein interactions.		 Manual
Database of protein interactomes [NHRI]
hp-DPI is a protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally.		 Manual

A liver cancer biomarker interactive curation system combining text mining and expert annotations [IASL]

  

This database serves as a research tool and an overview on variations of disease candidate genes [IASL]

  
     
Structural Genomics Databases
Structural Genomics Databases of Helicobacter pylori [NTHU]
HPSG is a bioinformatics web site for Helicobacter pylori. H. pylori is relatively small and suitable for a structural genomics and proteomics studies. Also, the genomes of the two unrelated strains – 26695 and J99 were sequenced in their entirety and are available for high-throughput, large-scale protein cloning and expression and little has been done on the proteomics especially structural genomics studies of H. pylori.		  
Structural Genomics Databases of Klebsiella pneumoniae [NTHU]  
Structural Genomics Databases of Stenotrophomonas maltophili [NTHU]  
Structural Genomics Databases of Xanthomonas campestris [NTHU]
XCC is an integrated structural and functional genomic project of Xanthomonas campestris, which is a plant pathogenic bacteria		  
     
Structure Databases
Circular Permutation Database [NTHU]
CPDB is the first database of circular permutants in proteins . 		 
Disulfide proteins database [NCTU]
SSDB, based on the hierarchical clustering scheme, clusters disulfide proteins according to their disulfide patterns can be used to detect the structural similarities of proteins of low sequence identities (<25%).		  

A web application for annotating biomedical entities and relations [IASL]