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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]. |
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| ===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]] |
- | **''EMBL'': The EMBL nucleotide sequence database including updates | + | *[[Protein databases]] |
- | **''REFSEQ'': Database providing non-redundant curated data representing knowledge of known genes | + | *[[Gene-related databases]] |
- | **''FANTOMn'': Database of mouse transcriptome | + | *[[Protein-related databases]] |
- | **''UTRnr'': 5-end and 3-end Untranslated Regions Database | + | *[[Ontology databases]] |
- | **''IMGT'': ImMunoGeneTics database. A database containing nucleotide sequences of immune system-related genes | + | *[[3D structures databases]] |
- | **''EMBLWGS'': The EMBL nucleotide sequence database - whole genome shotgun sequences | + | *[[Metabolic pathway databases]] |
- | **''REFSEQNEW'': Database providing non-redundant curated data representing knowledge of known genes RefSeq Updates | + | *[[Reference databases]] |
- | *'''PROTEIN databases''': | + | |
- | **''REFSEQP'': Database of protein information from NCBI | + | |
- | **''UNIPROT'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, **''REMTREMBL'': REM-TrEMBL (REMaining TrEMBL) contains translations of EMBL nucleotide sequences that will not be included in TrEMBL | + | |
- | **''UNIREF100'': Non redundant sequence database which combines identical sequences and sub-fragments from the same organism into a single UniRef entry | + | |
- | **''UNIREF90'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequence with at least 90% sequence identity | + | |
- | **''UNIREF50'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequences with at least 50% sequence identity | + | |
- | **''FANTOMp'': Database of translations of mouse transcriptome | + | |
- | **''IMGTHLA'': The IMGT/HLA Database is part of the international ImMunoGeneTics IMGT project | + | |
- | **''IPI'': International Protein Index - a top level guide to main proteome databases | + | |
- | **''REFSEQPNEW'': Database of protein information from REFSEQ RefSeq Protein Updates | + | |
- | **''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 | + | |
- | **''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''': | + | |
- | **''ENTREZGENE'': NCBI's database for gene-specific information. | + | |
- | **''EPD'': Eukariotic Promoter Database - Philipp Bucher (1996) | + | |
- | **''UNIGENE'': Unique gene cluster db from the NCBI | + | |
- | **''UNISEQ'': Sub-component of the UniGene db. Contains the sequence information from UniGene. | + | |
- | **''UTRSITE'': Sub-component of the UTRnr | + | |
- | **''HGBASE'': Human Genic Bi-Allelic Sequences Database | + | |
- | **''RHDB'': The RHDB Radiation Hybrid Mapping Submissions database | + | |
- | **''RHEXP'': The RHDB Radiation Hybrid Mapping Experimental Conditions database | + | |
- | **''RHMAP'': The RHDB Radiation Hybrid Map Information database | + | |
- | **''RHPANEL'': The RHPANEL RH Mapping panels database | + | |
- | | + | |
- | *'''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 | + | |
- | | + | |
- | *'''ONTOLOGIES databases''': | + | |
- | **''GOA'': Gene Ontology Annotation of UniProtKb | + | |
- | **''GO'': GO - Geneontology Database | + | |
- | *'''3D structures databases''': | + | |
- | **''NRL3D'': PIR-NRL3D Sequence-Structure Database. | + | |
- | **''PDB'': Protein Data Bank (PDB) - repository for the processing and distribution of 3-D biological macromolecular structure data | + | |
- | **''PDBFINDER'': Directory for the Brookhaven Protein Data Bank. Constructed from the PDB, DSSP and HSSP 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 | + | |
- | | + | |
| | | |
- | 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}} |