# server.dbfetch 2011-07-15 12:00:00

DB edam [
  method: dbfetch
  hasacc: N
  format: "obo"
  type: "text, obo"
  example: "0000352, 0001223"
  comment: "EMBRACE Data and Methods (EDAM) Ontology."
]

DB embl [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "M10051, K00650, D87894, AJ242600, HSINSR, HSFOS, ROD894, LOP242600, J00231.1, K00650.1, D87894.1, AJ242600.1"
  comment: "EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence resource. The main sources of the DNA and RNA sequences in the database are submissions from individual researchers, genome sequencing projects and patent applications."
]

DB emblcds [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "AAA59452, AAA59452.1"
  comment: "EMBLCDS is a database of nucleotide sequences of the CDS (coding sequence) features, as annotated in EMBL database. EMBLCDS record contains the nucleotide sequence of the CDS region, accompanying annotation from the parent nucleotide entry and the additional automatically generated annotation."
]

DB emblcon [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "CH003588, CH003588.1"
  comment: "The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries."
]

DB emblconexp [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "AL672111, AL672111.1"
  comment: "The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries. Expanded entries including the complete sequence."
]

DB emblsva [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "Y09633, Y09633.1, Y09633.4"
  comment: "The EMBL Sequence Version Archive is a repository of all entries which have ever appeared in the EMBL Nucleotide Sequence Database."
]

DB ensemblgene [
  method: dbfetch
  hasacc: N
  format: "embl, fasta, genbank, gff, gff3"
  type: "text, sequence, features"
  example: "ENSAMEG00000011969, ENSBTAG00000000988, ENSG00000139618, ENSMUSG00000041147"
  comment: "Ensembl genome databases for vertebrates and other eukaryotic species. Gene sequences and annotations."
]

DB ensembltranscript [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "ENSAMET00000013126, ENSBTAT00000001311, ENST00000380152, ENSMUST00000044620"
  comment: "Ensembl genome databases for vertebrates and other eukaryotic species. Transcript sequences."
]

DB epo_prt [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "A00022, A00022.1"
  comment: "Protein sequences appearing in patents from the European Patent Office (EPO)."
]

DB genomereviews [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "AE000784_GR, AE000784_GR.1"
  comment: "The Genome Reviews Database consists of curated versions of complete genome entries from the EMBL/GenBank/DDBJ nucleotide sequence database."
]

DB hgnc [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "1101, 3566, BRCA2, FACD"
  comment: "HUGO Gene Nomenclature Committee (HGNC) approved gene name and symbol (short-form abbreviation) for each human gene."
]

DB hgvbase [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "GEN000002654, IND000000198, SNP000002179, STR000008969"
  comment: "The Human Genic Bi-Allelic Sequences Database is an attempt to summarize all known sequence variations in the human genome and to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes."
]

DB imgthla [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "HLA00001"
  comment: "Sequences of the human major histocompatibility complex (HLA) including the official sequences for the WHO Nomenclature Committee For Factors of the HLA System."
]

DB imgthlap [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "HLA00001"
  comment: "Sequences of the human major histocompatibility complex (HLA) including the official sequences for the WHO Nomenclature Committee For Factors of the HLA System."
]

DB imgtligm [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "A00673"
  comment: "A comprehensive database of Immunoglobulins and T cell Receptors from human and other vertebrates."
]

DB interpro [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "IPR006212, IPR008266, IPR008957, IPR009030, IPR011009"
  comment: "The InterPro database (Integrated Resource of Protein Domains and Functional Sites) is an integrated documentation resource for protein families, domains and functional sites. It was developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects, but now also includes the SMART, TIGRFAMs, PIR SuperFamilies and most recently SUPERFAMILY databases."
]

DB ipdkir [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "KIR00001"
  comment: "A centralised repository for human Killer-cell Immunoglobulin-like Receptor (KIR) sequences."
]

DB ipdkirp [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "KIR00001"
  comment: "A centralised repository for human Killer-cell Immunoglobulin-like Receptor (KIR) sequences."
]

DB ipdmhc [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "MHC00001"
  comment: "Sequences of the the major histocompatibility complex in a number of species."
]

DB ipdmhcp [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "MHC00001"
  comment: "Sequences of the the major histocompatibility complex in a number of species."
]

DB ipi [
  method: dbfetch
  hasacc: N
  format: "fasta, swissprot"
  type: "text, features, sequence"
  example: "IPI00025803, IPI00220325, IPI00025803.3, IPI00220325.4"
  comment: "The International Protein Index (IPI) provides non-redundant proteome sets for a selection of higher eukaryotes, e.g. Arabidopsis, Chicken, Mouse, Human, etc. Cross-references are provided to the various source databases."
]

DB iprmc [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "A0A000"
  comment: "InterPro Matches Complete (IPRMC) for UniProtKB proteins."
]

DB iprmcuniparc [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "UPI0000000001"
  comment: "InterPro Matches Complete (IPRMC) for UniParc proteins."
]

DB jpo_prt [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "E50010"
  comment: "Protein sequences appearing in patents from the Japanese Patent Office (JPO)."
]

DB kipo_prt [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "DI500001"
  comment: "Protein sequences appearing in patents from the Korean Intellectual Property Office (KIPO)."
]

DB livelists [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "AF093062, AAC64372, 6019463, 6019464, AF093062.2, AAC64372.2"
  comment: "NCBI LiveLists provides a mapping between NCBI gi numbers and INSDC (i.e. DDBJ, EMBL-Bank and GenBank) accessions."
]

DB medline [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "1, 2859121, 17567924"
  comment: "MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The files contains over 11 million citations dating back to the mid-1960's, updated weekly."
]

DB nrnl1 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "NRN_DJ207917"
  comment: "Non-redundant patent nucleotides level-1. Nucleotide sequences from patents clustered by 100% sequence identity over whole length."
]

DB nrnl2 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "NRN006674C5"
  comment: "Non-redundant patent nucleotides level-2. Nucleotide sequences from patents clustered by patent family and then by 100% sequence identity over whole length."
]

DB nrpl1 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "NRP_AX013047"
  comment: "Non-redundant patent proteins level-1. Protein sequences from patents clustered by 100% sequence identity over whole length."
]

DB nrpl2 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "NRP00000001"
  comment: "Non-redundant patent proteins level-2. Protein sequences from patents clustered by patent family and then by 100% sequence identity over whole length."
]

DB pdb [
  method: dbfetch
  hasacc: N
  format: "fasta, pdb"
  type: "text, sequence"
  example: "101D, 1GAG, 10MH, 3E3Q, 3E3Q_A, 3E3Q_a, 3E3QA, 3E3Qa"
  comment: "Macromolecular structures from the Brookhaven Protein Data Bank (PDB). Contains protein and nucleotide structure and sequence data."
]

DB refseqn [
  method: dbfetch
  hasacc: N
  format: "fasta, refseq"
  type: "features, sequence"
  example: "AC_000162, NC_004952, NG_000865, NM_000231, NR_000003, NS_000188, NT_113950, NW_001030413, NZ_AAAC02000001, XM_001000025, XR_000302, 258513362, 32455353, 300797863, 209529740, AC_000162.1, NC_004952.1, NG_000865.5, NM_000231.2"
  comment: "The NCBI Reference Sequence project (RefSeq) provides reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins."
]

DB refseqp [
  method: dbfetch
  hasacc: N
  format: "fasta, refseqp"
  type: "features, sequence"
  example: "AP_000130, NP_862703, XP_001001333, YP_000022, ZP_00047513, 56160459, 32455307, AP_000130.1, NP_862703.1"
  comment: "The NCBI Reference Sequence project (RefSeq) provides reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins."
]

DB resid [
  method: dbfetch
  hasacc: N
  format: "pdb"
  type: "text, sequence"
  example: "AA0330"
  comment: "A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."
]

DB sgt [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "1, 283832, APC4091, IGBMC-0038-000, IPRv2949cPALZ, YCL050c"
  comment: "Structural Genomics Targets (SGT) is a protein target registration database, providing information on the experimental progress and status of target amino acid sequences selected for structural determination."
]

DB taxonomy [
  method: dbfetch
  hasacc: N
  format: "unknown"
  type: "text"
  example: "3702, 9606"
  comment: "Taxonomic classification of organisms for which there are sequences in the INSDC databases (i.e. DDBJ, EMBL-Bank and GenBank) and many other biological databases."
]

DB tracearchive [
  method: dbfetch
  hasacc: N
  format: "fasta, fastq"
  type: "sequence"
  example: "TI1, TI1941166100"
  comment: "An archive of capillary electrophoresis trace data."
]

DB uniparc [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "UPI0000000001, UPI0000046364, UPI00001B3DCE"
  comment: "The UniProt Archive (UniParc) contains available protein sequences collected from many different sources. The sequence data are archived to facilitate examination of changes to sequence data. Search UniParc if you want to examine the 'history' of a particular sequence."
]

DB uniprotkb [
  method: dbfetch
  hasacc: N
  format: "fasta, gff3, uniprot, uniprotxml"
  type: "text, features, sequence"
  example: "P06213, P29306, P68255, INSR_HUMAN, 1433X_MAIZE, 1433T_RAT"
  comment: "The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve “everything that is known” about a particular sequence."
]

DB uniref100 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "UniRef100_P06213"
  comment: "The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow the user to choose between a fast search and a truly comprehensive one."
]

DB uniref50 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "UniRef50_P06213"
  comment: "The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow the user to choose between a fast search and a truly comprehensive one."
]

DB uniref90 [
  method: dbfetch
  hasacc: N
  format: "fasta"
  type: "sequence"
  example: "UniRef90_P06213"
  comment: "The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow the user to choose between a fast search and a truly comprehensive one."
]

DB unisave [
  method: dbfetch
  hasacc: N
  format: "fasta, uniprot"
  type: "text, features, sequence"
  example: "P06213, P06213.157, P06213.3, INSR_HUMAN"
  comment: "The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions."
]

DB uspto_prt [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  type: "text, sequence, features"
  example: "AAA00053, I02590, AAA00053.1"
  comment: "Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO)."
]