SRS databases

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Aboout 70 DBs are locally mantained and available at CEINGE. [[SRS]] is used as the main web interface for accessing to these biological databases. 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.<br>+An automatic procedure, specifically developed, takes care to mantain the databases up to date: every night public servers are checked and, in case of new releases, the new file data are downloaded and automatically indexed.<br>
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. 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 [http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+databanks here].+The complete list of all the available databases on SRS is findable [http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+databanks here].
===Available databases=== ===Available databases===
Practically all the most used public databases are available, such as: Practically all the most used public databases are available, such as:
*[[DNA databases]] *[[DNA databases]]
- 
*[[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]]
-**''[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+GO GO]'': GO - Geneontology Database  
- 
*[[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.+*[[Metabolic pathway databases]]
-**''[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]]+
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PATHWAY PATHWAY]'': Kyoto Encyclopedia of Genes and Genomes (KEGG) +
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LENZYME LENZYME]'': Ligand Chemical Database for Enzyme Reactions+
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LCOMPOUND LCOMPOUND]'': Ligand Chemical Database for Enzyme Reactions+
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENZYME ENZYME]'': Database of enzyme nomenclature+
- +
*[[Reference databases]] *[[Reference databases]]
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+TAXONOMY TAXONOMY]'': Contains names of all organisms represented in sequence databases by at least one nucleotide or protein sequence 
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GENETICCODE GENETICCODE]'': NCBI database of genetic codes 
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+OMIM OMIM]'': Online Mendelian Inheritance in Man database.  
-**''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REBASE REBASE]'': Restriction Enzyme database. 
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Current revision

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 and, 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 findable here.

[edit] Available databases

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

Bioinformatics: Bioinfo Services: Bioinfo programs - Databases - Local facilities - Research DB
Retrieved from "http://mediawiki.ceinge.unina.it/index.php/SRS_databases"
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