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| - | More than 60 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 about 1 Tbyte (1000 Gigabytes) 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 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]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EMBL]'': The EMBL nucleotide sequence database including updates | + | *[[Protein databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQ]'': Database providing non-redundant curated data representing knowledge of known genes | + | *[[Gene-related databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+FANTOMn]'': Database of mouse transcriptome | + | *[[Protein-related databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UTRnr]'': 5-end and 3-end Untranslated Regions Database | + | *[[Ontology databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IMGT]'': ImMunoGeneTics database. A database containing nucleotide sequences of immune system-related genes | + | *[[3D structures databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EMBLWGS]'': The EMBL nucleotide sequence database - whole genome shotgun sequences | + | *[[Metabolic pathway databases]] |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQNEW]'': Database providing non-redundant curated data representing knowledge of known genes RefSeq Updates | + | *[[Reference databases]] |
| - | *'''PROTEIN databases''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQP]'': Database of protein information from NCBI | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': 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]'': 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]'': 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]'': 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]'': Database of translations of mouse transcriptome | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': 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]'': 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]'': 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]'': 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''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENTREZGENE]'': NCBI's database for gene-specific information. | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EPD]'': Eukariotic Promoter Database - Philipp Bucher (1996) | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIGENE]'': Unique gene cluster db from the NCBI | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': Sub-component of the UTRnr | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+HGBASE]'': Human Genic Bi-Allelic Sequences Database | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHDB]'': The RHDB Radiation Hybrid Mapping Submissions database | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHEXP]'': The RHDB Radiation Hybrid Mapping Experimental Conditions database | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHMAP]'': The RHDB Radiation Hybrid Map Information database | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHPANEL]'': The RHPANEL RH Mapping panels database | + | |
| - | | + | |
| - | *'''PROTEIN-related databases''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+INTERPRO]'': Integrated Resource of Protein Domains and Functional Sites | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': A Dictionary of Protein Sites and Patterns - A. Bairoch | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': Protein Motif Fingerprint Database | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': 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]'': 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 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 database. Seed alignments (hand edited) representing each domain | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PRODOM]'': A comprehensive collection of protein domain families | + | |
| - | | + | |
| - | *'''ONTOLOGIES databases''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GOA]'': Gene Ontology Annotation of UniProtKb | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GO]'': GO - Geneontology Database | + | |
| - | *'''3D structures databases''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+NRL3D]'': PIR-NRL3D Sequence-Structure Database. | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': 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]'': Kyoto Encyclopedia of Genes and Genomes (KEGG) | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LENZYME]'': Ligand Chemical Database for Enzyme Reactions | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LCOMPOUND]'': Ligand Chemical Database for Enzyme Reactions | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENZYME]'': Database of enzyme nomenclature | + | |
| - | *'''Reference databases''': | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+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]'': NCBI database of genetic codes | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+OMIM]'': Online Mendelian Inheritance in Man database. | + | |
| - | **''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REBASE]'': Restriction Enzyme database | + | |
| - | | + | |
| | | | |
| - | 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]. | + | {{footer|footername=footer biotools}} |
