Service Retirement

The EMBL-EBI SRS service was decommissioned on Thursday 19th December 2013. The tables below detail alternative services which provide access to the databanks and tools which have been available in SRS@EMBL-EBI.

For services provided by EMBL-EBI, please see EMBL-EBI Services. User with a programmatic/systematic usage requirement should also see the EMBL-EBI Web Services.

Instem, the developers of SRS, maintain a list of public SRS servers containing details of the databanks and tools provided by each SRS server. Users who require access via SRS should see the list to find alternative SRS servers.

If you have any queries about the retirement of the EMBL-EBI SRS service, please contact us via EMBL-EBI Support.

Databanks

Alternative sites which provide access to data which appeared in the SRS databanks, or provide equivalent data:

Library Group Databank Name Alternative Site
Active protein sequence databases BCIPEP http://www.imtech.res.in/raghava/bcipep/
EPO_PRTsee PATENT_PRT
IPI ftp://ftp.ebi.ac.uk/pub/databases/IPI/
IPIHISTORY ftp://ftp.ebi.ac.uk/pub/databases/IPI/
JPO_PRTsee PATENT_PRT
KIPO_PRTsee PATENT_PRT
NRPL1 http://www.ebi.ac.uk/patentdata/nr/, EBI Search/EB-eye, dbfetch/WSDbfetch
NRPL2 http://www.ebi.ac.uk/patentdata/nr/, EBI Search/EB-eye, dbfetch/WSDbfetch
PATENT_PRT http://www.ebi.ac.uk/patentdata/proteins, EBI Search/EB-eye, dbfetch/WSDbfetch
REFSEQPsee REFSEQ
REFSEQPROTNEWsee REFSEQ
REFSEQPROTRELsee REFSEQ
SWISSCHANGE http://www.uniprot.org/docs/humpvar.txt, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/swisschange/
USPO_PRTsee PATENT_PRT
CABRI - Animal and Human Cell Lines DSMZ_MUTZhttp://www.cabri.org/
ECACC_CELLhttp://www.cabri.org/
ICLChttp://www.cabri.org/
CABRI - Bacteria BCCM_LMGhttp://www.cabri.org/
CABI_BACThttp://www.cabri.org/
CBS_BACThttp://www.cabri.org/
CIP_BACThttp://www.cabri.org/
DSMZ_BACThttp://www.cabri.org/
NCCB_BACThttp://www.cabri.org/
NCIMB_BACThttp://www.cabri.org/
CABRI - DNA Probes ECACC_DNA_PROBEShttp://www.cabri.org/
CABRI - Fungi and Yeasts BCCM_IHEMhttp://www.cabri.org/
BCCM_MUCLhttp://www.cabri.org/
CABI_FILhttp://www.cabri.org/
CABI_YEASThttp://www.cabri.org/
CBS_FILhttp://www.cabri.org/
CBS_YEASThttp://www.cabri.org/
DSMZ_FUNGIhttp://www.cabri.org/
CABRI - HLA typed B Cell Lines ECACC_HLAhttp://www.cabri.org/
CABRI - Hybridomas ECACC_HYBRIDhttp://www.cabri.org/
CABRI - Phages DSMZ_PHAGEShttp://www.cabri.org/
NCCB_PHAGEShttp://www.cabri.org/
NCIMB_PHAGEShttp://www.cabri.org/
CABRI - Plant Cells DSMZ_PLANT_CELLhttp://www.cabri.org/
CABRI - Plant Viruses DSMZ_PLANT_VIRUSEShttp://www.cabri.org/
CABRI - Plasmids BCCM_LMBPhttp://www.cabri.org/
DSMZ_PLASMIDhttp://www.cabri.org/
NCCB_PLASMIDhttp://www.cabri.org/
Deprecated Protein Databases PIR http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
REMTREMBLsee UNIPARC
SWALL http://www.uniprot.org/, ftp://ftp.ebi.ac.uk/pub/databases/uniprot/ EBI Search/EB-eye, dbfetch/WSDbfetch
SWISSNEWsee SWALL
TREMBLNEWsee SWALL
EMBLCDS Grouped By EMBL_CDS_NR see CDSCLUSTERS
EMBLCDSBYGENENAME  
EMBLCDSBYEXON  
EMBLCDSBYINFERENCE  
EMBOSS Source Code EDATA ftp://emboss.open-bio.org/pub/EMBOSS/efunc/
EDATAREL ftp://emboss.open-bio.org/pub/EMBOSS/efuncrel/
EFUNC ftp://emboss.open-bio.org/pub/EMBOSS/efunc/
EFUNCREL ftp://emboss.open-bio.org/pub/EMBOSS/efuncrel/
Enzymes, reactions and metabolic pathways EMP  
ENZYME http://enzyme.expasy.org/, IntEnz, EBI Search/EB-eye
LCOMPOUNDhttp://www.genome.jp/ligand/
LENZYMEhttp://www.genome.jp/ligand/
LREACTIONhttp://www.genome.jp/ligand/
MPW2 
PATHWAY http://www.genome.jp/kegg/pathway.html
UCOMPOUNDhttp://umbbd.ethz.ch/
UENZYMEhttp://umbbd.ethz.ch/
UIMAGEMAPhttp://umbbd.ethz.ch/
UPATHWAYhttp://umbbd.ethz.ch/
UREACTIONhttp://umbbd.ethz.ch/
EUROFIR DKhttp://www.eurofir.net/
USDADERIVCODEhttp://www.eurofir.net/
USDADESChttp://www.eurofir.net/
USDAFOOTNOTEhttp://www.eurofir.net/
USDAGROUPhttp://www.eurofir.net/
USDANUTDATAhttp://www.eurofir.net/
USDANUTDEFhttp://www.eurofir.net/
USDASOURCECODEhttp://www.eurofir.net/
USDASOURCEShttp://www.eurofir.net/
USDASOURCESLINKShttp://www.eurofir.net/
USDAWEIGHThttp://www.eurofir.net/
Gene Dictionaries ENTREZGENE http://www.ncbi.nlm.nih.gov/gene
HGNC http://www.genenames.org/, EBI Search/EB-eye, dbfetch/WSDbfetch
HSAGENES http://www.genenames.org/, EBI Search/EB-eye, dbfetch/WSDbfetch
LOCUSLINK http://www.ncbi.nlm.nih.gov/gene
UNIGENE http://www.ncbi.nlm.nih.gov/UniGene/
UNILIB ftp://ftp.ncbi.nih.gov/repository/UniLib/
Gene Dictionaries and Ontologies EDAM http://edamontology.org/
Gene ontology resources GO http://www.geneontology.org/, QuickGO, EBI Search/EB-eye
GOA GOA, QuickGO, ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
Literature, Bibliography and Reference Databases GENETICCODE http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
MEDLINE Europe PubMed Central, PubMed Central, PubMed Central Canada, PubMed, EBI Search/EB-eye, dbfetch/WSDbfetch
MEDLINE2005see MEDLINE
MEDLINE2006see MEDLINE
MEDLINE2007see MEDLINE
MEDLINE2008see MEDLINE
MEDLINE2009see MEDLINE
MEDLINE2010see MEDLINE
MEDLINE2011see MEDLINE
MEDLINE2012see MEDLINE
MEDLINENEWsee MEDLINE
OMIM OMIM
PATABS Europe PubMed Central, Espacenet, EBI Search/EB-eye
PATENTEQUIVALENTS http://www.ebi.ac.uk/patentdata/, EBI Search/EB-eye, dbfetch/WSDbfetch
TAXONOMY ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/, European Nucleotide Archive (ENA), EBI Search/EB-eye, dbfetch/WSDbfetch
MED2PUB PubMed
Mapping RHDB http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHDB
RHEXP http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHEXP
RHMAP http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHMAP
RHPANEL http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHPANEL
MappingSub RHDBMAIN http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHDB
RHDBNEW http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+LibInfo+-lib+RHDB
Mutations ANDROGENR http://androgendb.mcgill.ca/, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/androgenr/
APC http://perso.curie.fr/Thierry.Soussi/APC.html
ARCGD http://seconde.scripps.edu/pdfarea/issue_22_96/0109a.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
ATM http://www.vmmc.org/vmrc/atm.htm
BIOMDB http://www.bh4.org/BH4DatabasesBiomdb.asp
BTKBASE http://bioinf.uta.fi/BTKbase/
CFTR http://www.genet.sickkids.on.ca/cftr/app
CD40LBASE http://bioinf.uta.fi/CD40Lbase/index.html
DMD http://www.dmd.nl/
EMBLCHANGE ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/emblchange/
EMD http://www.path.cam.ac.uk/emd/
FANCONI http://www.rockefeller.edu/fanconi/mutate/
FVII http://193.60.222.13/
G6PD http://seconde.scripps.edu/pdfarea/issue_15_97/beutler.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
GAA http://www.eur.nl/fgg/ch1/pompe/
GD http://seconde.scripps.edu/pdfarea/issue_01_98/beutler.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
GPI http://seconde.scripps.edu/pdfarea/issue_09_96/fujii.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
HAEMA http://europium.csc.mrc.ac.uk/WebPages/Main/main.htm, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/haema/
HAEMB http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/haemb/
HBVARS http://globin.cse.psu.edu/
HEHP http://seconde.scripps.edu/pdfarea/issue_20_96/0105a.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
HEREDSPHERO http://seconde.scripps.edu/pdfarea/issue_22_97/gallagher.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
HEXA http://www.debelle.mcgill.ca/hexa/
HGBASE https://www.gwascentral.org/, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/hgbase/
HGBASE_HAPLOTYPEsee HGBASE
HGBASE_SUBMITTERsee HGBASE
HUMAN_MITBASE 
HUMUT ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/humut/
IGF2R http://radonc.duke.edu/~jirtle/Database
IL2RGBASE http://research.nhgri.nih.gov/scid/
LDLR http://www.ucl.ac.uk/ldlr/Current/index.php?select_db=LDLR
MUTRES ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/mutres/
NCL http://www.ucl.ac.uk/ncl/
OMIMALLELE OMIM, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/omimallele/
OMIMOFFSET OMIM
OTC http://www.dcchildrens.com/cnmcresearch/disordersstudies/inbornerrors.aspx/
P16 http://pcdnr83.uio.no/
P53 http://www-p53.iarc.fr/index.html, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/p53/
P53B http://p53.free.fr/
P53LINK ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/p53link/
PAH http://www.pahdb.mcgill.ca/
PAX6 http://pax6.hgu.mrc.ac.uk/
PGK http://seconde.scripps.edu/pdfarea/issue_22_96/0108a.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
PK http://seconde.scripps.edu/pdfarea/issue_13_98/luciano.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
RB1 http://www.verandi.de/joomla/
RDS http://mol.ophth.uiowa.edu/MOL_WWW/Compendium.html
RHODOPSIN http://mol.ophth.uiowa.edu/MOL_WWW/Compendium.html
TPI http://seconde.scripps.edu/pdfarea/issue_06_96/schneid.pdf, ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/bcmd/
VWF http://www.vwf.group.shef.ac.uk/SSCsummary.html
XCGDBASE http://bioinf.uta.fi/CYBBbase/
Nucleotide related databases CDSCLUSTERS ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/emblcds/
CPGISLAND Ensembl
EMBLALIGN ftp://ftp.ebi.ac.uk/pub/databases/embl/align/
EPD http://epd.vital-it.ch/
MOUSE2HUMAN http://www.informatics.jax.org/
REBASE http://rebase.neb.com/rebase/rebase.html
TFCELL http://www.gene-regulation.com/pub/databases.html, ftp://ftp.ebi.ac.uk/pub/databases/transfac/
TFCLASSsee TFCELL
TFFACTORsee TFCELL
TFGENEsee TFCELL
TFMATRIXsee TFCELL
TFSITEsee TFCELL
UTR http://utrdb.ba.itb.cnr.it/
UTRSITE http://utrsite.ba.itb.cnr.it/
Nucleotide sequence databases EMBL European Nucleotide Archive (ENA), ENA Sequence Version Archive, EBI Search/EB-eye, dbfetch/WSDbfetch, ftp://ftp.ebi.ac.uk/pub/databases/embl/
EMBLANNsee EMBL
EMBLCDSsee EMBL
EMBLCONsee EMBL
EMBLCONEXPsee EMBL
EMBLIDACC ftp://ftp.ebi.ac.uk/pub/databases/embl/misc/entryname_to_acc.mapping
EMBLMGAsee EMBL
GENOMEREVIEWS ftp://ftp.ebi.ac.uk/pub/databases/genome_reviews/
GRGENESETS ftp://ftp.ebi.ac.uk/pub/databases/integr8/last_release/gene_sets/
GRTRANSCRIPTSETS ftp://ftp.ebi.ac.uk/pub/databases/integr8/last_release/transcript_sets/
IMGTHLA IMGT/HLA, ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/, EBI Search/EB-eye, dbfetch/WSDbfetch
IMGTLIGM IMGT/LIGM-db, ftp://ftp.ebi.ac.uk/pub/databases/imgt/LIGM-DB/, dbfetch/WSDbfetch
IPDKIR IPD-KIR, ftp://ftp.ebi.ac.uk/pub/databases/ipd/kir/, EBI Search/EB-eye, dbfetch/WSDbfetch
IPDMHC IPD-MHC, ftp://ftp.ebi.ac.uk/pub/databases/ipd/mhc/, EBI Search/EB-eye, dbfetch/WSDbfetch
REFSEQ http://www.ncbi.nlm.nih.gov/refseq/, dbfetch/WSDbfetch
LIVELISTS ftp://ftp.ncbi.nlm.nih.gov/genbank/livelists/
NRNL1 http://www.ebi.ac.uk/patentdata/nr/, EBI Search/EB-eye, dbfetch/WSDbfetch
NRNL2 http://www.ebi.ac.uk/patentdata/nr/, EBI Search/EB-eye, dbfetch/WSDbfetch
PATENT_DNAsee EMBL
Nucleotide sequence databases - subsections EMBLANNNEWsee EMBL
EMBLANNRELEASEsee EMBL
EMBLCONNEWsee EMBL
EMBLCONRELEASEsee EMBL
EMBLCONEXPNEWsee EMBL
EMBLCONEXPRELEASEsee EMBL
EMBLDELETEDRELEASEsee EMBL
EMBLESTRELEASEsee EMBL
EMBLNEWsee EMBL
EMBLRELEASEsee EMBL
EMBLTPAsee EMBL
EMBLTSAsee EMBL
EMBLTSANEWsee EMBL
EMBLTSARELEASEsee EMBL
EMBLWGSsee EMBL
EMBLWGSMASTERSsee EMBL
EMBLWGSNEWsee EMBL
EMBLWGSRELEASEsee EMBL
ENAPROJECT http://www.ncbi.nlm.nih.gov/bioproject, European Nucleotide Archive (ENA)
REFSEQGENNEWsee REFSEQ
REFSEQGENRELsee REFSEQ
Other BIOCATAL ftp://ftp.ebi.ac.uk/pub/databases/bio_catal/
GETFT 
Protein function databases INTERPRO InterPro, EBI Search/EB-eye, dbfetch/WSDbfetch
IPRMATCHESsee IPRMC
IPRMC InterPro, ftp://ftp.ebi.ac.uk/pub/databases/interpro/, dbfetch/WSDbfetch
IPRMATCHES_ENSEMBLsee IPRMC_UNIPARC
IPRMC_UNIPARC InterPro, ftp://ftp.ebi.ac.uk/pub/databases/interpro/, dbfetch/WSDbfetch
NICEDOM http://prodom.prabi.fr/
PEP 
PFAMA http://pfam.sanger.ac.uk/
PFAMBsee PFAMA
PFAMCsee PFAMA
PFAMSEEDsee PFAMA
PRINTS http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
PRODOM http://prodom.prabi.fr/
PROSITE http://prosite.expasy.org/
PROSITEDOCsee PROSITE
Protein interaction databases (IntAct) INTACTACTOR IntAct, ftp://ftp.ebi.ac.uk/pub/databases/intact/ EBI Search/EB-eye
INTACTEXPsee INTACTACTOR
INTACTINTsee INTACTACTOR
Protein structure databases DSSP http://swift.cmbi.ru.nl/gv/dssp/, ftp://ftp.ebi.ac.uk/pub/databases/dssp/
FSSP ftp://ftp.ebi.ac.uk/pub/databases/fssp/, http://ekhidna.biocenter.helsinki.fi/dali/
HSSP http://swift.cmbi.ru.nl/gv/hssp/ ftp://ftp.ebi.ac.uk/pub/databases/hssp/
PDB http://www.pdb.org/, http://www.ebi.ac.uk/pdbe/, EBI Search/EB-eye, dbfetch/WSDbfetch
PDBFINDER http://swift.cmbi.ru.nl/gv/pdbfinder/, ftp://ftp.ebi.ac.uk/pub/databases/pdb_finder/
RESID http://pir.georgetown.edu/resid/
SGT http://sbkb.org/tt/
UniProt Universal Protein Resource SWISSPROTsee UNIPROT
SPTREMBLsee UNIPROT
UNIPARCsee UNIPROT
UNIPROT http://www.uniprot.org/, ftp://ftp.ebi.ac.uk/pub/databases/uniprot/, EBI Search/EB-eye, dbfetch/WSDbfetch
UNIPROTXMLsee UNIPROT
UNIREF100see UNIPROT
UNIREF50see UNIPROT
UNIREF90see UNIPROT

Analysis Tools

Replacement services for the anlaysis tools which were available in SRS@EMBL-EBI.

Package Tool Name Alternative Site
CLUSTAL ClustalW2 ClustalW 2, http://www.clustal.org/
NClustalW2 ClustalW 2, http://www.clustal.org/
EMBOSS all Wageningen Bioinformatics EMBOSS Explorer, BIPS EMBOSS GUI, Mobyle@Pasteur, Soaplab2 Vital-IT Web Services, http://emboss.open-bio.org/
FASTA FASTA FASTA, FASTA at UVa
SSEARCH SSEARCH, FASTA at UVa
NCBI BLAST BLASTN NCBI BLAST, BLAST at NCBI
BLASTP NCBI BLAST, BLAST at NCBI
BLASTX NCBI BLAST, BLAST at NCBI
OTHER InterProScan InterPro, InterProScan 4
MPsrch SSEARCH
Restrictionmap see EMBOSS tool remap