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a Nucleotide Databases

  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.		  
  A database index for the genome summarized information [NCTU]

 

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
  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.
       

a Protein Databases

 

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 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		  

a Structure Databases

 

 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%). 		 
     
 
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