Databases and Data Collections

At the moment, the Supercomputing Institute has hosted numerous public and project-specific databases and data collections in various computational laboratories. For example, sequence databases are loaded at the Institute's servers. These include 1): Flat file databases (genbank, embl, swissprot, PIR), 2): NCBI BLAST databases (nt, est_human, est_mouse, est_others, patnt, pdbnt, nr, swissprot, pataa, pdbaa etc.), 3): Genome databases (Human, Mouse, Rat, Chicken, Bovine, Fugu, Zerbafish, Drosophila, Yeast, E. coli etc.), and 4): Other specific databases including these user specified databases. Most of these databases will be updated regularly.

Public Databases and Data Collections

Field of Science	Project	Description	Access
Biology	NCBI BLAST databases	Nucleotide Sequence Database Collaboration for BLAST	/usr/local/db/blast/current at CGL, BSCL, SDVL, VWL
Biology	Genbank	International Nucleotide Sequence Database Collaboration	/usr/local/db/genbank/current at BSCL
Biology	Ensembl Genomes	Genomic, cDNA, and Protein sequence data for human, rat, mouse, etc.	/usr/local/db/current/current BLAST at BSCL, CGL, SDVL, VWL
Biology	Ensembl MySQL databases	Ensembl MySQL databases for human, rat, mouse, etc.	Connect to ensembl MySQL database at SDML
Biology	Databases for GCG and EMBOSS	Genebank, Genpeptide, Uni-Prot, and Refseq databases.	/usr/local/db/gcgdb/current GCG and EMBOSS at CGL
Biology	Pfam	Protein families database of aligments and HMMS	/usr/local/db/pfam/current HMMER at CGL and BSCL
Biology	Protein Data Bank	Single worldwide respository for the processing and distribution of 3-D biological macromolecular structure data	/usr/local/db/pdb/current InsightII at BSCL, CGL, SDVL, VWL
Biology	Gene Ontology	Controlled vocabulary to describe gene and gene product attributes in any organism	SDML
Biology	International Protein Index	Proteomes of higher eukaryotic organisms	/usr/local/db/macotdb Mascot at CGL
Biology	MSDB	Mass spectrometry protien sequence database	/usr/local/db/mascotdb/MSDB/current Mascot at CGL
Biology	InterPro database	Collection of PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR superfamily, SUPERFAMILY, Gene3D, and PANTHER databases.	InterProScan at CGL
Biology	Uniprot	Uniprot (Universal Protein Resource), comprehensive catalog of information on proteins.	/usr/local/db/blast/current BLAST, GCG, and EMBOSS at CGL

Project-Specific Databases and Data Collections

Field of Science	Project	Description	Access
Biology	Microarray Data System	Data system for distributing Affymetrix microarray data	Operated by AHC Biomedical Genomics Center X500 login or guest login
Biology	Sequence Data System	Data system for distributing Sequencing data	Operated by AHC Biomedical Genomics Center X500 login or guest login
Biology	Bio-image Data System	Data system for distributing Bio-Image data	Operated by CBS Imaging Center X500 login or guest login
Biology	Computational Proteomics	Data system for distributing Mass Spectrometry data	Operated by Center for Mass Spectrometry and Proteomics X500 login or guest login
Biology	Microarray Database	Microarray Database	Operated by Arkady Khodursky's group username/password protected
Biology	Sequence Management and Annotation Databases	Data system for annotating sequence data	Operated by Wei-Shou Hu's group username/password protected
Biology	Microarray Database	Microarray Database	Operated by Dr. Wei-Shou Hu's group username/password protected