MAGNet: Databases

 

Editor's note: The MAGNet center formally closed in July 2016, following the mandatory conclusion of its grant after more than 10 years of activity. The pages in this section constitute an archive of its work.

A number of bioinformatics databases are produced by C2B2/MAGNet groups. These include databases of structure, function, localization, and regulation. In addition, copies of many major databases from outside sources such as the NCBI are maintained locally for searches on facility computers. Finally, the HICCC Oncogenomics Core provides access to several commercial microarray database and analysis tools.

Locally produced databases (C2B2) 

Database Lab Details Access
CNKB Califano et al. Cellular Network Knowledge Base (B-cell and other datasets) geWorkbench
Functional_AnnotationDB Honig Annotation on PDB structures and the results from programs such as DALI and SKAN geWorkbench
HMAP Honig Hybrid multidimensional alignment of profiles. /razor/0/databases/hmap/1dprof
LOC3d Rost Predicted subcellular LOCalizations for eukaryotic proteins of known 3D structure LOC3d
ER-GolgiDB Rost Proteins predicted to localize to the Endoplasmic Reticulum or Golgi Apparatus ER-GolgiDB
PEP Rost Prediction of protein structural characteristics for Entire Proteomes PEP
LOChom Rost Predicted subcellular LOCalizations based on sequence homology to experimentally annotated proteins. LOChom
CellCycleDB Rost Proteins predicted to take park in Cell Cycle Control CellCycleDB
LOCtarget Rost Predicted sub-cellular LOCalization for structural genomics targets. LOCtarget
DSSPcontDB Rost Secondary structure of proteins assigned according to the continuum method. DSSPcontDB
LOCkey Rost Predicted LOCalization for proteins of entire proteomes. LOCkey
Epitome Rost Sequences and structures of antigens and the antibodies that interact with them. Epitome
NMP-db Rost Nuclear Matrix-Associated Proteins. NMP-db
NLSdb Rost Nuclear localization signals (NLSs) and nuclear proteins (external derivation) NLSdb
Geneways Rzhetsky Molecular pathway data automatically extracted from research literature. Geneways ,  geWorkbench
ADOMETA Vitkup ADoption of Orphan METabolic Activities ADOMETA

External DBs locally maintained or modified

Database Lab Details Access
BIG Rost Combines the PDB, Uniprot, and TrEMBL databases. /data/derived/big/big

Major external databases installed locally

Database Details Locations* C2B2 External Link
Sequence
GenBank  (via GCG) Comprehensive, annotated DNA sequence database from the NIH 2   GenBank
NCBI BlastDB Nucleic acid and peptide sequences formatted for local BLAST searches. 1   Blast
GenPept Translated protein-coding sequences derived from GenBank DNA entries. 1, 2    
UniProt Combines protein sequence, function, classification and cross-reference entries from Swiss-Prot, TrEMBL, and PIR. Includes clustering (UniRef). 1, 2   UniProt
Genomes of Individual Species Individual genomes are available on request on C2B2 servers. Major genomes including Human, Mouse, Rat etc. are always available.  1   Genomes at NCBI
Structure and Patterns
SCOP Detailed and comprehensive description of all known protein structures. 1 /razor/0/databases/scop1.71  SCOP
PDB 3D structural coordinates for proteins and complexes  1 /razor/0/databases/pdb PDB ,  geWorkbench
PROSITE  Sequence patterns of structural and functional motifs  2   PROSITE
Pfam  Statistical models of sequences comprising protein domains  1, 2    Pfam
REBASE  Patterns of restriction enzyme binding and cutting  1, 2    REBASE
PQS Protein Quaternary Structure database  1 /razor/0/databases/macmol/ PQS
Pathway and Vocabulary
KEGG Kyoto Encyclopedia of Genes and Genomes, available through Pathway Architect application 2   KEGG
GeneOntology (GO)  Controlled vocabulary, available through Pathway Architect application  2   GO ,  geWorkbench

* Location key: (1) C2B2, (2) HICC.

HICCC - Commercial database and analysis systems

Database Company Details Local Access
GeneTraffic Stratagene Local microarray data repository and analysis GeneTraffic
GeneSpring Agilent Microarray data analysis through facility
ArrayAssist Stratagene Microarray data analysis through facility
PathwayArchitect Stratagene Pathway analysis using curated and extracted information from literature. through facility