SRS databases

From Wiki CEINGE

Revision as of 20:22, 25 June 2007 by Giovanni (Talk | contribs)
Jump to: navigation, search

Aboout 70 DBs are locally mantained and available at CEINGE. SRS is used as the main web interface for accessing to these biological databases. An automatic procedure specifically developed takes care to mantain the databases up to date: every night public servers are checked for the presence of new releases: in case of new releases, the new file data are downloaded and automatically indexed.
Through SRS, more than 60 public databases are available at CEINGE, stored as flat-files on a dedicated file server, for a total of over 2 terabyte of HD space.

The complete list of all the available databases on SRS is available here.

Available databases

Practically all the most used public databases are available, such as:

  • Protein-related databases
    • INTERPRO: Integrated Resource of Protein Domains and Functional Sites
    • IPRMATCHES: All hits to Swiss-Prot and TrEMBL entries in which the signatures are found by INTERPRO
    • PROSITE: A Dictionary of Protein Sites and Patterns - A. Bairoch
    • BLOCKS: The Blocks database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
    • PRINTS: Protein Motif Fingerprint Database
    • PFAMA: The A division (human curated) division of the Pfam database. Alignments of protein domains and conserved regions.
    • PFAMB: The B division (automatically clustered) division of the Pfam database. Alignments of protein domains and conserved regions
    • SWISSPFAM: An annotated description of how Pfam domains map to (possibly multidomain) SwissProt entries.
    • PFAMHMM: PfamHmm database. Database of the Hidden Markov Models (HMMs) derived from the seed alignment in Pfam.
    • PFAMSEED: PfamSeed database. Seed alignments (hand edited) representing each domain
    • PRODOM: A comprehensive collection of protein domain families
  • 3D structures databases
    • NRL3D: PIR-NRL3D Sequence-Structure Database.
    • PDB: Protein Data Bank (PDB) - repository for the processing and distribution of 3-D biological macromolecular structure data
    • PDBFINDER: Directory for the Brookhaven Protein Data Bank. Constructed from the PDB, DSSP and HSSP databases
  • Reference databases
    • TAXONOMY: Contains names of all organisms represented in sequence databases by at least one nucleotide or protein sequence
    • GENETICCODE: NCBI database of genetic codes
    • OMIM: Online Mendelian Inheritance in Man database.
    • REBASE: Restriction Enzyme database.
Bioinformatics: Bioinfo Services: Bioinfo programs - Databases - Local facilities - Research DB
Retrieved from "http://mediawiki.ceinge.unina.it/index.php/SRS_databases"
Personal tools