SRS databases
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| *[[Protein-related databases]] | *[[Protein-related databases]] | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+INTERPRO INTERPRO]'': Integrated Resource of Protein Domains and Functional Sites | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IPRMATCHES IPRMATCHES]'': All hits to Swiss-Prot and TrEMBL entries in which the signatures are found by INTERPRO | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PROSITE PROSITE]'': A Dictionary of Protein Sites and Patterns - A. Bairoch | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+BLOCKS BLOCKS]'': The Blocks database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PRINTS PRINTS]'': Protein Motif Fingerprint Database | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMA PFAMA]'': The A division (human curated) division of the Pfam database. Alignments of protein domains and conserved regions. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMB PFAMB]'': The B division (automatically clustered) division of the Pfam database. Alignments of protein domains and conserved regions | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+SWISSPFAM SWISSPFAM]'': An annotated description of how Pfam domains map to (possibly multidomain) SwissProt entries. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMHMM PFAMHMM]'': PfamHmm database. Database of the Hidden Markov Models (HMMs) derived from the seed alignment in Pfam. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMSEED PFAMSEED]'': PfamSeed database. Seed alignments (hand edited) representing each domain | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PRODOM PRODOM]'': A comprehensive collection of protein domain families | ||
| - | |||
| *[[Ontology databases]] | *[[Ontology databases]] | ||
| **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GOA GOA]'': Gene Ontology Annotation of UniProtKb | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GOA GOA]'': Gene Ontology Annotation of UniProtKb | ||
Revision as of 20:24, 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:
- 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.
