Databanks and tools supported in SRS

This page lists the databanks and tools officially supported in SRS for which BioWisdom provides regular updates and maintenance. Please remember that due to its dynamic nature SRS allows the integration of many more data sources (see the List of Public SRS installation for a a list of the ones we know about).

If you have a request for a new database or tool to be added to the list or are interested on how to integrate your own data into SRS please email srs_support@biowisdom.com

Libraries in SRS currently supported by Instem Scientific
DatasetDescription /
Member database names in SRS (between brackets: display name)
UniProtKB (Flat File)UniProt protein sequence knowledgebase
http://www.uniprot.org
UNIPROT (UniProtKB)
UNIPROTVARSPLICE (UniProtKB Splice Isoforms)
UNIPROT_SWISSPROT (UniProtKB/Swiss-Prot)
UNIPROT_TREMBL (UniProtKB/TrEMBL)
EMBL (Flat File)EMBL primary DNA sequence database
http://www.ebi.ac.uk/embl/
EMBL
EMBLCDS
EMBLCDSRELEASE
EMBLCDSNEW
EMBLRELEASE (EMBL (Release))
EMBLNEW (EMBL (Updates))
EMBLWGS (EMBL (Whole Genome Shotgun Sequences))
EMBLWGSRELEASE (EMBL (Whole Genome Shotgun Sequences - full release))
EMBLWGSNEW (EMBL (Whole Genome Shotgun Sequences - updates))
GenBank (Flat File)NCBI primary DNA sequence database
http://www.ncbi.nlm.nih.gov/genbank/
GENBANK
GENBANKRELEASE (GENBANK (Release))
GENBANKNEW (GENBANK (Updates))
GENBANKWGS (GENBANK (Whole Genome Shotgun))
DDBJ (Flat File)DDBJ primary DNA sequence database
http://www.ddbj.nig.ac.jp/
DDBJ
DDBJRELEASE (DDBJ (Release))
DDBJNEW (DDBJ (Updates))
DDBJWGS (DDBJ (Whole Genome Shotgun))
RefSeq (Flat File)NCBI non-redundant curated DNA sequence database
http://www.ncbi.nlm.nih.gov/RefSeq/
REFSEQ (RefSeq)
REFSEQVARIATIONS
REFSEQRELEASE (RefSeq (Release))
REFSEQNEW (RefSeq (Updates))
REFSEQVARIATIONS1
REFSEQVARIATIONS2
REFSEQVARIATIONS3
REFSEQVARIATIONS4
RefSeqP (Flat File)NCBI non-redundant curated Protein sequence database
http://www.ncbi.nlm.nih.gov/RefSeq/
REFSEQP (RefSeq Protein)
REFSEQPRELEASE (RefSeq Protein (Release))
REFSEQPNEW (RefSeq Protein (Updates))
NCBI NR (Flat File)NCBI (not completely) non-redundant sets of fasta sequences taken from all major sequence databases
ftp://ftp.ncbi.nih.gov/blast/db/README
NR
NT
GIMAP
MEDLINE (Flat File)MEDLINE is the National Library of Medicine's premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences.
http://www.nlm.nih.gov/databases/databases_medline.html
MEDLINE (Medline)
MEDLINERELEASE (Medline Full Release)
MEDLINENEW
MEDLINENEWFILES
MEDLINEUPDATES (Medline Updates)
MED2PUB (Medline to Pubmed)
PubChem (XML)NCBI database of chemical structures of small organic molecules and information on their biological activities
Added to SRS8.3 in September 2010
http://pubchem.ncbi.nlm.nih.gov/
PUBCHEMCOMPOUND (PubChem Compounds)
PUBCHEMSUBSTANCE (PubChem Substances)
PUBCHEMASSAYRESULT
PUBCHEMASSAY
Entrez Gene (XML)NCBI's database for gene-specific information
http://www.ncbi.nlm.nih.gov/gene
ENTREZGENE
PDB (Flat File)Protein Data Bank - Biological Macromolecular Structures
http://www.pdb.org/pdb/home/home.do
GenPept (Flat File)Protein sequence database translated from GenBank
ftp://ftp.ncifcrf.gov/pub/genpept/announce.txt
GENPEPT
GENPEPTRELEASE (GENPEPT (Release))
GENPEPTNEW (GENPEPT (Updates))
GeneSeq (Flat File)Sequences from worldwide patents
PATENTNUMBERS added to SRS8.3 in March 2008
http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq
NAGENESEQ (GENESEQ (Nucleic Acid))
AAGENESEQ (GENESEQ (Peptide))
NAGENESEQSUPP (GENESEQ Supplement (Nucleic Acid))
AAGENESEQSUPP (GENESEQ Supplement (Peptide))
FASTASEQP
FASTASEQN
PATENTNUMBERS (GeneSeq Patent Numbers)
IMGT/LIGM-DB (Flat File)Immunoglobulin DNA sequence database
http://imgt.cines.fr/
IMGTLIGM (IMGT/LIGM-DB)
CCDS (Flat File)Consensus Coding Sequences
http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi
CCDSNUC (CCDS (Nucleotide))
CCDSPROT (CCDS (Protein))
UniGene (Flat File)Database of gene clusters
http://www.ncbi.nlm.nih.gov/unigene
UNIGENE
UNISEQ
UNIEST
UniLib (Flat File)Unified Library of EST and SAGE clusters
ftp://ftp.ncbi.nih.gov/repository/UniLib/
dbEST (Flat File)Expressed Sequence Tags database
http://www.ncbi.nlm.nih.gov/dbEST/
dbSTS (Flat File)database of Sequence Tagged Sites
http://www.ncbi.nlm.nih.gov/dbSTS/
dbGSS (Flat File)Genome Survey Sequences Database
http://www.ncbi.nlm.nih.gov/dbGSS/
GENETICCODE (Flat File)CDS translation tables for various taxons from the NCBI
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
TAXONOMY (Flat File)NCBI Taxonomy database
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
OMIM (Flat File)Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/omim
dbSNP (Flat File)NCBI database off Single Nucleotide Polymorphism
Added to SRS8.3 in March 2008
http://www.ncbi.nlm.nih.gov/projects/SNP/index.html
DBSNP
DBSNPLOCATION
HomoloGene (XML)Database of homologs among the annotated genes of several completely sequenced eukaryotic genomes
http://www.ncbi.nlm.nih.gov/homologene
KEGG (Flat File)Kyoto Encyclopedia of Genes and Genomes (and also pathways, compounds..)
Kegg Disease was added to SRS8.3 in Feb 2010
http://www.genome.jp/kegg/ http://www.pathway.jp
KEGGGENES_AA (KEGG Genes (Amino Acid))
KEGGGENES_NA (KEGG Genes (Nucleic Acid))
LCOMPOUND
LDRUG
LENZYME
LGLYCAN
LREACTION
KEGGGENOME (KEGG Genome)
KEGGORTHOLOGY (KEGG Orthology)
KEGGDISEASE (KEGG Disease)
PATHWAY
DrugBank (Flat File)Database of drugs and their targets
Added to SRS8.3 in Sep 2009
http://www.drugbank.ca/
DRUGBANKPARTNER (DrugBank (Partners))
DRUGBANK (DrugBank (Drugs))
HMDB (Flat File)Human Metabolome Database
Added to SRS8.3 in Oct 2009
http://www.hmdb.ca/
HMDB (HMDB Metabolites)
HMDBPROTEIN (HMDB Enzymes)
Reactome (RDB)A curated knowledgebase of biological pathways
http://www.reactome.org/
(Not maintained by Prisma)
ChEBI (RDB)Chemical Entities of Biological Interest
http://www.ebi.ac.uk/chebi/
(Not maintained by Prisma)
CHEBI (ChEBI)
ChEMBL (RDB)Database of bioactive drug-like small molecules
Added to SRS8.3 in March 2010
http://www.ebi.ac.uk/chembldb/index.php
(Not maintained by Prisma)
CHEMBLBIOACTIVITY (ChEMBL Bioactivities)
CHEMBLCOMPOUND (ChEMBL Compounds)
CHEMBLTARGET (ChEMBL Targets)
UniRef (XML)UniProt Reference Clusters
http://www.ebi.ac.uk/uniref/
UNIREF100
UNIREF90
UNIREF50
InterPro (XML)Integrated database of predictive protein "signatures"
http://www.ebi.ac.uk/interpro/
IPRMATCHES
INTERPRO
PROSITE (Flat File)Database of protein domains, families and functional sites
http://www.expasy.ch/prosite/
PROSITE
PROSITEDOC
PRINTS (Flat File)Compendium of protein fingerprints
http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/index.php
Pfam (Flat File)Collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
http://pfam.sanger.ac.uk/
PFAMA
PFAMB
PFAMC
PFAMHMM
PFAMSEED
SWISSPFAM
ENZYME (Flat File)Enzyme nomenclature database
http://expasy.org/enzyme/
EPD (Flat File)Eukaryotic Promoter Database
http://www.epd.isb-sib.ch/
GeneCards (Flat File)Database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes
http://www.genecards.org/index.shtml
PDBFINDER (Flat File)The PDBFINDER database holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries
http://swift.cmbi.kun.nl/gv/pdbfinder/
CATH (Flat File)Manually curated classification of protein domain structures
http://www.cathdb.info/
DSSP (Flat File)The DSSP database of secondary structure assignments of PDB entries.
http://swift.cmbi.kun.nl/gv/dssp/
HSSP (Flat File)Homology-derived Secondary Structure of Proteins
http://swift.cmbi.kun.nl/gv/hssp/
FSSP (Flat File)Families of Structurally Similar Proteins
http://en.wikipedia.org/wiki/Families_of_structurally_similar_proteins
REBASE (Flat File)Restriction Enzyme Database
http://rebase.neb.com/rebase/rebase.html
REBASE
REBCOMM
RESID (Flat File)RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Added to SRS8.3 in January 2011
http://www.ebi.ac.uk/RESID/
MEROPS (RDB)The peptidase database
Added to SRS8.3 in Dec 2009
http://merops.sanger.ac.uk/
(Not maintained by Prisma)
MEROPSPRO
MEROPSSEQ
MEROPSFAM
MEROPSSMI
IntAct (XML)Database for protein interaction data
http://www.ebi.ac.uk/intact/main.xhtml
INTACTINTERACTION (INTACT Interaction)
INTACTINTERACTOR (INTACT Interactor)
INTACTEXPERIMENT (INTACT Experiment)
BioGRID (XML)Database of Protein and Genetic Interactions
http://thebiogrid.org/
BIOGRIDINTERACTION (BIOGRID Interaction)
BIOGRIDINTERACTOR (BIOGRID Interactor)
BIOGRIDEXPERIMENT (BIOGRID Experiment)
MINT (XML)Molecular INTeraction database
http://mint.bio.uniroma2.it
MINTINTERACTION (MINT Interaction)
MINTINTERACTOR (MINT Interactor)
MINTEXPERIMENT (MINT Experiment)
DIP (XML)the Database of Interacting Proteins
http://dip.doe-mbi.ucla.edu
(Not maintained by Prisma)
DIPINTERACTION (DIP Interaction)
DIPINTERACTOR (DIP Interactor)
DIPEXPERIMENT (DIP Experiment)
IREFINDEX (Flat File)iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID.
http://irefindex.uio.no/wiki/iRefIndex
Gene Ontology (XML)Ontology of genes and gene products (XML version)
http://www.geneontology.org/
GO
Gene Ontology (RDB)Ontology of genes and gene products (MySql version)
http://www.geneontology.org/
(Not maintained by Prisma)
GOTERM (GO Terms)
GOGENPROD (GO Gene Products)
Ensembl (RDB)Genome databases for various species
http://www.ensembl.org/
(Not maintained by Prisma)
EnsemblGene (EnsemblGene (All Species))
HumanGene
MouseGene
RatGene
DogGene
ZebrafishGene
C_elegansGene
ChimpGene
FruitflyGene
MosquitoGene
PufferfishGene
User End user owned libraries to store sequence information in SRS for analysis ot to annotate entries in other databases
 
USERDNA (My Nucleotide Sequences)
USERPROTEIN (My Protein Sequences)
Data Display/Export These are databases which are invisible to the user, but which are used for data display, or to provide export functionality in certain data formats
 
UNIPROTXML UNIPROT_SWISSPROTXML UNIPROT_TREMBLXML INTACTMITAB BIOGRIDMITAB MINTMITAB DIPMITAB PDBML PDBCIF DRUGBANKSDF HMDBSDF MESH chebivert chebidown EnsemblTranscript HumanTranscript MouseTranscript RatTranscript DogTranscript ZebrafishTranscript C_elegansTranscript ChimpTranscript FruitflyTranscript MosquitoTranscript PufferfishTranscript EnsemblMarker HumanMarker MouseMarker RatMarker DogMarker ZebrafishMarker EnsemblAffy HumanAffy MouseAffy RatAffy DogAffy ZebrafishAffy C_elegansAffy ChimpAffy FruitflyAffy MosquitoAffy EnsemblSeq HumanSeq MouseSeq RatSeq DogSeq ZebrafishSeq C_elegansSeq ChimpSeq FruitflySeq MosquitoSeq PufferfishSeq EnsemblKar HumanKar MouseKar RatKar Compara
Data Management These are databases which are invisible to the user, but which are used in data management by prisma
 
MEDLINEDELETED PATHWAYTAR GENECARDSTAR RESIDDATA REFSEQFILES REFSEQPFILES EMBLNEWFILES EMBLWGSNEWFILES GBNEWFILES DDBJNEWFILES CHEBICHEMSEARCH INTACTDATA BIOGRIDDATA MINTDATA
PATENT_PRT (Flat File)Protein sequences from patent submissions to the US, European, Korean and Japanese patent offices.
Added to SRS8.3 in February 2011
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/README
PATENT_PRT (Patent Proteins)
NRPAT (Flat File)Non redundant patent sequence databases available from the EBI
Added to SRS8.3 in July 2012
http://www.ebi.ac.uk/patentdata/nr/
NRPL1 (NR Patent Proteins - level 1)
NRPL2 (NR Patent Proteins - level 2)
NRNL1 (NR Patent DNA - level 1)
NRNL2 (NR Patent DNA - level 2)
PATENTEQUIVALENTS (Patent Equivalents)
COSMIQ (Flat File)Catalogue Of Somatic Mutations In Cancer
Added to SRS8.3 in February 2011
http://www.sanger.ac.uk/genetics/CGP/cosmic/
COSMICSEQ
COSMICGENE
COSMICTUMOUR
59 datasets231 libraries
Most Flat file and XML databases listed here can be maintaind using SRS Prisma. Prisma cannot maintain RDB databases.
Databases marked as 'Added in SRS8.3' are not supported for earlier versions of SRS.
Libraries in SRS no longer maintained by Instem Scientific
These are datasets which are no longer maintained or to which we no longer have access. We still provide parsers, frozen at the last version for which we had access. These parser will probably not be included in future versions of SRS
DatasetDescription /
Member database names in SRS (between brackets: display name)
IPI (Flat File)International Protein Index
No longer updated/maintained - last release in September 2011
http://www.ebi.ac.uk/IPI/IPIhelp.html
BLOCKS (Flat File)Database of multiple aligned ungapped segments corresponding to the most highly conserved regions of proteins
No longer updated/maintained - last release in April 2007
http://blocks.fhcrc.org/blocks/help/about_blocks.html
ProDom (Flat File)Cmprehensive set of protein domain families automatically generated from the UniProt Knowledge Database
No access to latest version of data - frozen at last public release (May 2006)
http://prodom.prabi.fr/prodom/current/html/home.php
DOMO (Flat File)Database of aligned protein domains
No longer updated/maintained - last release in 1998
http://abcis.cbs.cnrs.fr/domo/
RHdb (Flat File)The Radiation Hybridization Database
No longer updated/maintained - last release in 2001
ftp://ftp.ebi.ac.uk/pub/databases/RHdb/
RHPANEL
RHMAP
RHEXP
RHDB
TransFac (Flat File)Transcription factor Database
No access to the latest version of the data - frozen at April 2007
http://www.biobase-international.com/
TFSITE
TFCELL
TFFACTOR
TFCLASS
TFGENE
TFMATRIX
TFFRAGMENT
TransPath (XML)Pathway Database
No access to the latest version of the data - frozen at April 2007
http://www.biobase-international.com/
TRANSPATHPATHWAY (TRANSPATH Pathway)
TRANSPATHREACTION (TRANSPATH Reaction)
TRANSPATHMOLECULE (TRANSPATH Molecule)
TRANSPATHREFERENCE (TRANSPATH Reference)
TRANSPATHAnnotate (TRANSPATH Annotate)
TRANSPATHGENE (TRANSPATH Gene)
BIND (XML)Biomolecular Interaction Network Database.
No longer available
http://www.bind.ca
BINDInteraction (BIND Interaction)
BINDPathway (BIND Pathway)
BINDComplex (BIND Complex)
Tools in SRS currently supported by Instem Scientific
Tool groupDescription/
Tool names in SRS
BLASTBasic Local Alignment Search Tool
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
BLASTP BLASTX BLASTN TBLASTX TBLASTN PSIBLAST ALIPSIBLAST CONTPSIBLAST BL2SEQ
FASTAThe FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml
FASTA NFASTA FASTX FASTY TFASTA TFASTX TFASTY SSEARCH GLSEARCH GGSEARCH
HMMERBiosequence analysis using profile hidden Markov models
http://hmmer.janelia.org/
HMMSEARCH HMMSCAN HMMBUILD
ClustalWGeneral purpose multiple sequence alignment program for DNA or proteins
http://www.ebi.ac.uk/Tools/clustalw2/index.html
CLUSTALW NCLUSTALW CLUSTALO
MUSCLEMUltiple Sequence Comparison by Log-Expectation
Added in the initial release of SRS8.3
http://www.ebi.ac.uk/Tools/muscle/
PMUSCLE NMUSCLE
QuickTreeBuilding huge Neighbour-Joining trees of protein sequences.
Added to SRS8.3 in Jan 2008
http://www.sanger.ac.uk/resources/software/quicktree/
QUICKTREE NQUICKTREE
tacgFast command line application for pattern matching and analysis of nucleic acids and protein
http://sourceforge.net/projects/tacg/
RESTRICTIONMAP
EMBOSSThe European Molecular Biology Open Software Suite
http://emboss.sourceforge.net/
ANTIGENIC BACKTRANSEQ BACKTRANAMBIG BANANA BIOSEDN BIOSEDP BTWISTED CAI CHAOS CHARGE CHECKTRANS CHIPS COMPSEQN COMPSEQP CONSAMBIGP CONSAMBIGN CONSN CONSP CPGPLOT CPGREPORT CUSP CUTSEQN CUTSEQP DAN DEGAPSEQN DEGAPSEQP DESCSEQN DESCSEQP DENSITY DIFFSEQN DIFFSEQP DISTMATN DISTMATP DOTMATCHERN DOTMATCHERP DOTPATHN DOTPATHP DOTTUPN DOTTUPP DREG EDIALIGNN EDIALIGNP EINVERTED EPESTFIND EPRIMER3 EPRIMER32 EPRIMERS EQUICKTANDEM EST2GENOME ETANDEM EXTRACTSEQN EXTRACTSEQP FREAKN FREAKP FUZZNUC FUZZPRO FUZZTRAN GARNIER GEECEE GETORF HELIXTURNHELIX HMOMENT IEP INFOALIGNN INFOALIGNP INFOSEQN INFOSEQP ISOCHORE JASPSCAN MARSCAN MASKSEQN MASKAMBIGNUC MASKAMBIGPROT MASKSEQP MATCHERN MATCHERP MEGAMERGER MERGERN MERGERP MSBARN MSBARP NEEDLEALLN NEEDLEALLP NEEDLEN NEEDLEP NEWCPGREPORT NEWCPGSEEK OCTANOL PALINDROME PASTESEQN PASTESEQP PATMATDB PATMATMOTIFS PEPCOIL PEPDIGEST PEPINFO PEPNET PEPSTATS PEPWHEEL PEPWINDOW PEPWINDOWALL PLOTCONN PLOTCONP PLOTORF POLYDOTN POLYDOTP PREG PRETTYPLOTN PRETTYPLOTP PRETTYSEQ PSCAN RECODER REMAP RESTOVER RESTRICT REVSEQ SEQMATCHALLN SEQMATCHALLP SEQRETN SEQRETP SHOWALIGNN SHOWALIGNP SHOWORF SHOWPEP SHOWSEQ SHUFFLESEQN SHUFFLESEQP SIGCLEAVE SILENT SIXPACK SIRNA SPLITTERN SPLITTERP STRETCHERN STRETCHERP SUPERMATCHERN SUPERMATCHERP SYCO TCODE TFSCAN TMAP TRANSEQ TRIMEST TRIMSEQN TRIMSEQP UNIONN UNIONP VECTORSTRIP WATERN WATERP WOBBLE WORDCOUNTN WORDCOUNTP WORDMATCHN WORDMATCHP WORDFINDERN WORDFINDERP FDNACOMP FDNADIST FDNAML FDNAMLK FDNAPARS FDNAPENNY FFITCH FKITSCH FPROML FPROMLK FPROTDIST FNEIGHBOR FPROTPARS
PrintScanSearch of PRINTS database for matching fingerprints
http://www.bioinf.manchester.ac.uk/fingerPRINTScan/
PRINTSCAN
ChemicalSearchChemical Structure searching using OpenBabel
Added to SRS8.3 in September 2010
http://openbabel.org/wiki/Main_Page
CHEMICALSEARCH
10 tool groups202 tools