SRS databases
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| *[[Protein databases]] | *[[Protein databases]] | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQP REFSEQP]'': Database of protein information from NCBI | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT UNIPROT]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REMTREMBL REMTREMBL]'': REM-TrEMBL (REMaining TrEMBL) contains translations of EMBL nucleotide sequences that will not be included in TrEMBL | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF100 UNIREF100]'': Non redundant sequence database which combines identical sequences and sub-fragments from the same organism into a single UniRef entry | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF90 UNIREF90]'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequence with at least 90% sequence identity | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF50 UNIREF50]'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequences with at least 50% sequence identity | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+FANTOMp FANTOMp]'': Database of translations of mouse transcriptome | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IMGTHLA IMGTHLA]'': The IMGT/HLA Database is part of the international ImMunoGeneTics IMGT project | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IPI IPI]'': International Protein Index - a top level guide to main proteome databases | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQPNEW REFSEQPNEW]'': Database of protein information from REFSEQ RefSeq Protein Updates | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT_SWISSPROT UNIPROT_SWISSPROT]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. UniProt/Swissprot contains manually-annotated records with information extracted from literature and curator-evaluated computational analysis | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT_TREMBL UNIPROT_TREMBL]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. UniProt/Trembl consists of computationally analyzed records that await full manual annotation | ||
| - | |||
| *[[Gene-related databases]] | *[[Gene-related databases]] | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENTREZGENE ENTREZGENE]'': NCBI's database for gene-specific information. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EPD EPD]'': Eukariotic Promoter Database - Philipp Bucher (1996) | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIGENE UNIGENE]'': Unique gene cluster db from the NCBI | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNISEQ UNISEQ]'': Sub-component of the UniGene db. Contains the sequence information from UniGene. | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UTRSITE UTRSITE]'': Sub-component of the UTRnr | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+HGBASE HGBASE]'': Human Genic Bi-Allelic Sequences Database | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHDB RHDB]'': The RHDB Radiation Hybrid Mapping Submissions database | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHEXP RHEXP]'': The RHDB Radiation Hybrid Mapping Experimental Conditions database | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHMAP RHMAP]'': The RHDB Radiation Hybrid Map Information database | ||
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHPANEL RHPANEL]'': The RHPANEL RH Mapping panels database | ||
| *[[Protein-related databases]] | *[[Protein-related databases]] | ||
Revision as of 20:22, 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:
- 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
- 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.
