Libraries in SRS currently supported by Instem Scientific | ||
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Dataset | Description | 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)) EMBLWGSHUM (EMBL WGS - Human)) EMBLWGSMUS (EMBL WGS - Mouse) EMBLWGSROD (EMBL WGS - Rodent) EMBLWGSMAM (EMBL WGS - Mammalian)) EMBLWGSVRT (EMBL WGS - Vertebrate) EMBLWGSINV (EMBL WGS - Invertebrate) EMBLWGSPLN (EMBL WGS - Plant) EMBLWGSFUN (EMBL WGS - Fungal) EMBLWGSPRO (EMBL WGS - Prokaryote) EMBLWGSENV (EMBL WGS - Environmental) EMBLWGSVRL (EMBL WGS - Viral) EMBLWGSUNC (EMBL WGS - Unclassified) EMBLWGSRELEASE (EMBL (Whole Genome Shotgun Sequences - full release)) EMBLWGSNEW (EMBL (Whole Genome Shotgun Sequences - updates)) EMBLWGSMASTER (EMBL WGS - MASTER Records) |
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)) GENBANKWGSMASTER (GENBANK (Whole Genome Shotgun - Master records)) GENBANKWGSFILES |
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 | PDB |
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/ | UNILIB |
dbEST (Flat File) | Expressed Sequence Tags database http://www.ncbi.nlm.nih.gov/dbEST/ | DBEST |
dbSTS (Flat File) | database of Sequence Tagged Sites http://www.ncbi.nlm.nih.gov/dbSTS/ | DBSTS |
dbGSS (Flat File) | Genome Survey Sequences Database http://www.ncbi.nlm.nih.gov/dbGSS/ | DBGSS |
GENETICCODE (Flat File) | CDS translation tables for various taxons from the NCBI http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi | GENETICCODE |
TAXONOMY (Flat File) | NCBI Taxonomy database http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ | TAXONOMY |
OMIM (Flat File) | Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/omim | 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 DBSNPVCF_HUMAN DBSNPVCFHUMANDATA DBSNPVCF_OTHER |
HomoloGene (XML) | Database of homologs among the annotated genes of several completely sequenced eukaryotic genomes http://www.ncbi.nlm.nih.gov/homologene | 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) | REACTOME |
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 | PRINTS |
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/ | ENZYME |
EPD (Flat File) | Eukaryotic Promoter Database http://www.epd.isb-sib.ch/ | EPD |
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/ | PDBFINDER |
CATH (Flat File) | Manually curated classification of protein domain structures http://www.cathdb.info/ | CATH |
DSSP (Flat File) | The DSSP database of secondary structure assignments of PDB entries. http://swift.cmbi.kun.nl/gv/dssp/ | DSSP |
HSSP (Flat File) | Homology-derived Secondary Structure of Proteins http://swift.cmbi.kun.nl/gv/hssp/ | HSSP |
FSSP (Flat File) | Families of Structurally Similar Proteins http://en.wikipedia.org/wiki/Families_of_structurally_similar_proteins | FSSP |
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/ | 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 | 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 RESIDDATA REFSEQFILES REFSEQPFILES EMBLNEWFILES EMBLWGSHUMFILES EMBLWGSMUSFILES EMBLWGSRODFILES EMBLWGSMAMFILES EMBLWGSVRTFILES EMBLWGSINVFILES EMBLWGSPLNFILES EMBLWGSFUNFILES EMBLWGSPROFILES EMBLWGSENVFILES EMBLWGSVRLFILES EMBLWGSUNCFILES EMBLWGSFILES 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/ (Not maintained by Prisma) |
COSMICSEQ COSMICGENE COSMICTUMOUR |
58 datasets | 260 libraries |
Libraries in SRS no longer maintained by Instem Scientific | ||
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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 | ||
Dataset | Description | 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 | IPI |
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 | BLOCKS |
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 | PRODOM |
DOMO (Flat File) | Database of aligned protein domains No longer updated/maintained - last release in 1998 http://abcis.cbs.cnrs.fr/domo/ | 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 | ||
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Tool group | Description | Tool names in SRS |
BLAST | Basic 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 |
FASTA | The 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 |
HMMER | Biosequence analysis using profile hidden Markov models http://hmmer.janelia.org/ |
HMMSEARCH HMMSCAN HMMBUILD |
ClustalW | General purpose multiple sequence alignment program for DNA or proteins http://www.ebi.ac.uk/Tools/clustalw2/index.html |
CLUSTALW NCLUSTALW CLUSTALO |
MUSCLE | MUltiple Sequence Comparison by Log-Expectation Added in the initial release of SRS8.3 http://www.ebi.ac.uk/Tools/muscle/ |
PMUSCLE NMUSCLE |
QuickTree | Building huge Neighbour-Joining trees of protein sequences. Added to SRS8.3 in Jan 2008 http://www.sanger.ac.uk/resources/software/quicktree/ |
QUICKTREE NQUICKTREE |
tacg | Fast command line application for pattern matching and analysis of nucleic acids and protein http://sourceforge.net/projects/tacg/ |
RESTRICTIONMAP |
EMBOSS | The 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 |
PrintScan | Search of PRINTS database for matching fingerprints http://www.bioinf.manchester.ac.uk/fingerPRINTScan/ |
PRINTSCAN |
ChemicalSearch | Chemical Structure searching using OpenBabel Added to SRS8.3 in September 2010 http://openbabel.org/wiki/Main_Page |
CHEMICALSEARCH |
10 tool groups | 202 tools |