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EBIEMBL-EBI Web Serviceshelpdatabases

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Table of Contents

Available databases

Dbfetch

Databases available through WSDbfetch:

Database Description dbfetch name
EMBL 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. embl
EMBL CDS 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. emblcds
EMBL Sequence Version Archive The EMBL Sequence Version Archive is a repository of all entries which have ever appeared in the EMBL Nucleotide Sequence Database. emblsva
EMBL Contig The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries. emblcon
EMBL Annotated cons This database contains Annotated EMBLCON entries emblann
UniProt Knowledgebase 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. uniprot
Genome Reviews The Genome Reviews Database consists of curated versions of complete genome entries from the EMBL/GenBank/DDBJ nucleotide sequence database. genomereviews
HGVBASE 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. hgvbase
InterPro 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. interpro
UniProt Clusters 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. uniref50, uniref90, uniref100
UniProt Archive 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. uniparc
UniProtKB Version Archive The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. unisave
International Protein Index 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. ipi
Protein Structure Sequences Protein sequences from structures described in the Brookhaven Protein Data Bank (PDB) pdb
EPO Patent Protein Sequences Protein sequences appearing in patents from the European Patent Office (EPO) epo_prt
JPO Patent Protein Sequences Protein sequences appearing in patents from the Japanese Patent Office (JPO) jpo_prt
KIPO Patent Protein Sequences Protein sequences appearing in patents from the Korean Intellectual Property Office (KIPO) kipo_prt
USPTO Patent Protein Sequences Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO) uspto_prt
Medline 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. medline
RefSeq Genome The NCBI Reference Sequence project (RefSeq) will provide reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. refseq
RefSeq Proteome The NCBI Reference Sequence project (RefSeq) will provide reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. refseqp

Also see the getSupportedDBs operation provided by the service.

Similarity & Homology Search Databases

Note: the sequence similarity search services now implement meta-information methods to get the details of the available databases.

Protein databases

DB Name Description Tools
uniprot UniProt Knowledgebase NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
swissprot UniProtKB/Swiss-Prot NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
uniref100 UniProt Clusters 100% NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
uniref90 UniProt Clusters 90% NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
uniref50 UniProt Clusters 50% NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
uniparc UniProt Archive NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
ipi International Protein Index NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
pdb Protein Structure Sequences NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
sgt Structural Genomics Targets NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
intact IntAct NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
imgthlap IMGT/HLA NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
epop EPO Patent Protein Sequences NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
jpop JPO Patent Protein Sequences NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
kpop KIPO Patent Protein Sequences NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA
uspop USPTO Patent Protein Sequences NCBI BLAST, PSI-BLAST, PHI-BLAST, WU-BLAST, FASTA

Nucleotide databases

These are the nucleotide databases you can use with our homology searches web services:

DB Name Description Tools
embl EMBL Database NCBI BLAST, WU-BLAST, FASTA
em_rel EMBL Release NCBI BLAST, WU-BLAST, FASTA
emnew EMBL Updates NCBI BLAST, WU-BLAST, FASTA
emcds EMBL Coding Sequence NCBI BLAST, WU-BLAST, FASTA
em_rel_env EMBL Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_est_env EMBL EST Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_env EMBL GSS Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_env EMBL HTG Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_env EMBL Patent Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_std_env EMBL Standard Environmental NCBI BLAST, WU-BLAST, FASTA
em_rel_fun EMBL Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_est_fun EMBL EST Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_fun EMBL GSS Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_fun EMBL HTC Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_fun EMBL HTG Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_fun EMBL Patent Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_std_fun EMBL Standard Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_fun EMBL STS Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_fun EMBL TPA Fungi NCBI BLAST, WU-BLAST, FASTA
em_rel_hum EMBL Human NCBI BLAST, WU-BLAST, FASTA
em_rel_est_hum EMBL EST Human NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_hum EMBL GSS Human NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_hum EMBL HTC Human NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_hum EMBL HTG Human NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_hum EMBL Patent Human NCBI BLAST, WU-BLAST, FASTA
em_rel_std_hum EMBL Standard Human NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_hum EMBL STS Human NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_hum EMBL TPA Human NCBI BLAST, WU-BLAST, FASTA
em_rel_inv EMBL Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_est_inv EMBL EST Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_inv EMBL GSS Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_inv EMBL HTC Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_inv EMBL HTG Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_inv EMBL Patent Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_std_inv EMBL Standard Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_inv EMBL STS Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_inv EMBL TPA Invertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_mam EMBL Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_est_mam EMBL EST Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_mam EMBL GSS Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_mam EMBL HTC Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_mam EMBL HTG Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_mam EMBL Patent Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_std_mam EMBL Standard Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_mam EMBL STS Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_mam EMBL TPA Mammal NCBI BLAST, WU-BLAST, FASTA
em_rel_mus EMBL Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_est_mus EMBL EST Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_mus EMBL GSS Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_mus EMBL HTC Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_mus EMBL HTG Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_mus EMBL Patent Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_std_mus EMBL Standard Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_mus EMBL STS Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_mus EMBL TPA Mouse NCBI BLAST, WU-BLAST, FASTA
em_rel_phg EMBL Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_phg EMBL GSS Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_phg EMBL HTG Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_phg EMBL Patent Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_std_phg EMBL Standard Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_phg EMBL TPA Phage NCBI BLAST, WU-BLAST, FASTA
em_rel_pln EMBL Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_est_pln EMBL EST Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_pln EMBL GSS Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_pln EMBL HTC Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_pln EMBL HTG Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_pln EMBL Patent Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_std_pln EMBL Standard Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_pln EMBL STS Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_pln EMBL TPA Plant NCBI BLAST, WU-BLAST, FASTA
em_rel_pro EMBL Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_est_pro EMBL EST Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_pro EMBL GSS Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_pro EMBL HTC Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_pro EMBL HTG Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_pro EMBL Patent Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_std_pro EMBL Standard Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_pro EMBL STS Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_pro EMBL TPA Prokaryote NCBI BLAST, WU-BLAST, FASTA
em_rel_rod EMBL Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_est_rod EMBL EST Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_rod EMBL GSS Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_rod EMBL HTC Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_rod EMBL HTG Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_rod EMBL Patent Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_std_rod EMBL Standard Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_rod EMBL STS Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_rod EMBL TPA Rodent NCBI BLAST, WU-BLAST, FASTA
em_rel_syn EMBL Synthetic NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_syn EMBL Patent Synthetic NCBI BLAST, WU-BLAST, FASTA
em_rel_std_syn EMBL Standard Synthetic NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_syn EMBL TPA Synthetic NCBI BLAST, WU-BLAST, FASTA
em_rel_tgn EMBL Transgenic NCBI BLAST, WU-BLAST, FASTA
em_rel_std_tgn EMBL Standard Transgenic NCBI BLAST, WU-BLAST, FASTA
em_rel_unc EMBL Unclassified NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_unc EMBL Patent Unclassified NCBI BLAST, WU-BLAST, FASTA
em_rel_std_unc EMBL Standard Unclassified NCBI BLAST, WU-BLAST, FASTA
em_rel_vrl EMBL Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_vrl EMBL GSS Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_vrl EMBL HTG Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_vrl EMBL Patent Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_std_vrl EMBL Standard Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_vrl EMBL TPA Viral NCBI BLAST, WU-BLAST, FASTA
em_rel_vrt EMBL Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_est_vrt EMBL EST Vertebrate NCBI BLAST, WU-BLAST, FASTA
em_rel_gss_vrt EMBL GSS Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_htc_vrt EMBL HTC Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_htg_vrt EMBL HTG Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_pat_vrt EMBL Patent Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_std_vrt EMBL Standard Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_sts_vrt EMBL STS Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa_vrt EMBL TPA Vertibrate NCBI BLAST, WU-BLAST, FASTA
em_rel_est EMBL Expressed Sequence Tag NCBI BLAST, WU-BLAST, FASTA
em_rel_gss EMBL Genome Survey Sequence NCBI BLAST, WU-BLAST, FASTA
em_rel_htc EMBL High Throughput cDNA NCBI BLAST, WU-BLAST, FASTA
em_rel_htg EMBL High Throughput Genome NCBI BLAST, WU-BLAST, FASTA
em_rel_pat EMBL Patent NCBI BLAST, WU-BLAST, FASTA
em_rel_std EMBL Standard NCBI BLAST, WU-BLAST, FASTA
em_rel_sts EMBL Sequence Tagged Site NCBI BLAST, WU-BLAST, FASTA
em_rel_tpa EMBL Third Party Annotation NCBI BLAST, WU-BLAST, FASTA
emall EMBL Release and Updates NCBI BLAST, WU-BLAST, FASTA
evec EMBL Vectors NCBI BLAST, WU-BLAST, FASTA
imgtligm IMGT/LIGM-DB NCBI BLAST, WU-BLAST, FASTA
imgthla IMGT/HLA NCBI BLAST, WU-BLAST, FASTA

Parasite databases

These are the nucleotide databases you can use with our WU-BLAST web service:

DB Name Description Tools
nem Nematoda WU-BLAST
fil Filarial WU-BLAST
brugia B.malayi WU-BLAST
oncv O.volvulus WU-BLAST
apicom Apicomplexa WU-BLAST
plas Plasmodium WU-BLAST
plasf P.falciparum WU-BLAST
toxo T.gondii WU-BLAST
crypto C.parvum WU-BLAST
eimeria Eimeria WU-BLAST
kineto Kinetoplastids WU-BLAST
schisto Schistosoma WU-BLAST
schunq Schisto unique WU-BLAST
mansoni S.mansoni WU-BLAST
jap S.japonicum WU-BLAST
cercunq Cerc unique WU-BLAST
japunq Jap unique WU-BLAST
entamoeba entamoeba WU-BLAST
bgESTnr bgESTnr WU-BLAST

ASD databases

The Alternative Splicing Database (ASD) is a database of alternatively spliced exons.

Note: the Alternative Splicing Database (ASD) and the Alternative Transcript Diversity database (ATD) have been merged into a single resource: the Alternative Splicing and Transcript Diversity database (ASTD). You may wish to use the ASTD databases instead of these.

DB Name Description Tools
altsgen Splice Genes WU-BLAST
altsiso Splice Patterns WU-BLAST
aedb AEDB exons WU-BLAST
apdb Peptides WU-BLAST

ASTD databases

The Alternative Splicing and Transcript Diversity database (ASTD) merges the Alternative Splicing Database (ASD) and Alternative Transcript Diversity database (ATD) into a single resource.

DB Name Description Tools
astdi ASTD Isoforms WU-BLAST
astdg ASTD Gene WU-BLAST
astdp ASTD Peptides WU-BLAST

LGIC databases

Ligand Gated Ion Channel Database.

DB Name Description Tools
lgicp Ligand Gated Ion Channel Database Protein FASTA
lgicn Ligand Gated Ion Channel Database Nucleotide FASTA
 
help/databases.1271933402.txt · Last modified: 2010/04/22 12:05 (external edit)
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