SRS databases

From Wiki CEINGE

Revision as of 20:24, 25 June 2007 (edit) Giovanni (Talk | contribs) ← Previous diff		Revision as of 20:25, 25 June 2007 (edit) (undo) Giovanni (Talk | contribs) Next diff →
Line 16:		Line 16:
	*[[3D structures databases]]		*[[3D structures databases]]
-	**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+NRL3D NRL3D]'': PIR-NRL3D Sequence-Structure Database.
-	**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PDB PDB]'': Protein Data Bank (PDB) - repository for the processing and distribution of 3-D biological macromolecular structure data
-	**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PDBFINDER PDBFINDER]'': Directory for the Brookhaven Protein Data Bank. Constructed from the PDB, DSSP and HSSP databases
	*[[Methabolic pathway databases]]		*[[Methabolic pathway databases]]

---

Revision as of 20:25, 25 June 2007

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:

• DNA databases

• Protein databases
• Gene-related databases

• Protein-related databases
• Ontology databases

• 3D structures databases

• Methabolic pathway databases
  • PATHWAY: Kyoto Encyclopedia of Genes and Genomes (KEGG)
  • LENZYME: Ligand Chemical Database for Enzyme Reactions
  • LCOMPOUND: Ligand Chemical Database for Enzyme Reactions
  • ENZYME: Database of enzyme nomenclature

• 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