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Protein Motif and Protein Domain Prediction Protein motiv og Protein Domain Fremskrivning

Also See Our Link Database of Protein Motif Bioinformatic Tools Se også vores link database Protein Motif Bioinformatic Tools

Protein motifs and domains are important as they provide clues as to posible functions of the protein, and possible interactions of the protein. Protein motiver og domæner er vigtige som de giver fingerpeg med hensyn til muligt funktioner af proteinet, og de mulige vekselvirkninger mellem protein. If the protein for example has a domain for DNA binding, you would predict that that protein may act by binding to DNA sequences. Hvis det protein for eksempel har et domæne til DNA-bindende, ville du forudsige, at dette protein kan handle ved at binde sig til DNA-sekvenser.

A note on protein motif and protein domain database searches: Most proteins are modular with several domains.  If your protein or unknown proteni is most similar to a protein kinase, this does not necessarily mean that it is a kinase - it is possible the two proteins share several other domains (ie. several SH3 domains). Et notat om protein motiv og protein domæne database søgninger: De fleste proteiner er modulopbyggede med flere domæner. Hvis din protein eller ukendte proteni er mest ligner et protein kinase, dette betyder ikke nødvendigvis, at det er en kinase - det er muligt de to proteiner aktie adskillige andre domæner (dvs. flere SH3 domæner).

See Our Link Database of Protein Motif Bioinformatic Tools Se vores link database Protein Motif Bioinformatic Tools

Protein Motif Databases: Protein Motif Databaser:

CDD The Conserved Domain Database. CDD De bevares Domain Database. Proteins often contain several modules or domains, each with a distinct evolutionary origin and function. Proteiner ofte indeholde flere moduler eller domæner, hver med et særskilt evolutionære oprindelse og funktion. NCBI's Conserved Domain Database is a collection of multiple sequence alignments for ancient domains and full-length proteins. NCBI's bevares Domain Database er en samling af flere sekvens tilnaermelser for gamle domæner, og i fuld længde proteiner. The CD-Search service may be used to identify the conserved domains present in a protein query sequence. Cd-Search-tjenesten kan bruges til at identificere de bevares domæner til stede i et protein query sekvens.

CDD Keyword Search Search the Conserved Domain Database by Keyword at Entrez Pubmed. CDD Keyword Search Search the bevares Domain Database af søgeord på Entrez Pubmed.

CDART: Conserved Domain Architecture Retrieval Tool CDART: bevares Domain Architecture Retrieval Tool

InterPro InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. InterPro InterPro er en database af protein familier, domæner og funktionelle sites, hvor identificeres funktioner, der findes i kendte proteiner kan anvendes på ukendt protein sekvenser.

PROSite PROSITE is a database of protein families and domains. PROSite PROSITE er en database af protein familier og domæner. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. Den består af biologisk væsentlige steder, mønstre og profiler, der medvirker til at pålideligt identificere hvilken kendt protein familien (hvis nogen) en ny sekvens tilhører.

Pfam Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam Pfam er en stor samling af flere sekvens tilnaermelser og skjulte Markov modeller dækker mange fælles protein domæner. Pfam version 7.7b (October 2002) contains alignments and models for 4832 protein families, based on the Swissprot 40 and SP-TrEMBL Pfam version 7.7b (oktober 2002) indeholder tilnaermelser og modeller til 4.832 protein familier, der er baseret på Swissprot 40 og SP-TrEMBL

ProDom Protein Domain Database ProDom Protein Domain Database

PairsDB The Automatic Domain Decomposition Algorithm (ADDA) is used to generate a database of protein domain families with complete coverage of all protein sequences. PairsDB Automatic Domain nedbrydning Algoritme (Adda) bruges til at generere en database over protein domæne familier med fuldstændig dækning af alle protein-sekvenser. Sequences are split into domains and domains are grouped into protein domain families in a completely automated process. Sequences er delt op i områder og områder er inddelt i protein domæne familier i en fuldstændig automatiseret proces. The current database contains domains for more than 1.5 million sequences in more than 40 000 domain families. Den aktuelle database indeholder domæner for mere end 1,5 mio sekvenser i mere end 40 000 domæne familier. In particular, there are 3828 novel domain families that do not overlap with the curated domain databases Pfam, SCOP and InterPro. Især er der 3828 nye domæne familier, der ikke overlappe de kurateret domæne databaser Pfam, Scop og InterPro. Data isfreely available for downloading and querying via a web interface. Data isfreely rådighed til downloading og søgninger via en web-grænseflade. See also: Se også:
PairsDB Domain Families Search PairsDB Domain Familier Søg
PairsDB Domain Families Browse PairsDB Domain Familier Gennemse

PRINTS PRINTS is a compendium of protein fingerprints. PRINTS PRINTS er et kompendium af protein fingeraftryk. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Et fingeraftryk er en gruppe bevares motiver brugt til at karakterisere et protein familie; dets diagnostiske magt er raffineret af iterativ scanning af en SWISS-PROT/TrEMBL komposit. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Normalt er de motiver, ikke overlapper hinanden, men er adskilt langs en sekvens, selvom de kan være sammenhængende i 3D-rummet. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. Fingeraftryk kan indkode protein folds og funktioner mere fleksibelt og kraftigere end kan enkelt motiver, fuld diagnostisk potens som følge af den gensidige sammenhæng med motiv naboer.

HITS Motif Scan Hits is a free database devoted to protein domains. Hits Motif Scan Hits er en gratis database, der afsættes til protein-domæner. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. Det er også en samling af værktøjer til undersøgelse af forholdet mellem protein sekvenser og motiver beskrevet på dem. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models Disse motiver er defineret ved en heterogen samling af indikatorer, som i dag omfatter regulære udtryk, generaliserede profiler og skjulte Markov modeller

SMART Simple Modular Architecture Research Tool.  Goal: to allow automatic identification and annotation of domains in user-supplied protein sequences. SMART Simple Modular Architecture Research Tool. Mål: at lade de automatiske identifikation og påtegning af domæner i user-leverede protein sekvenser.

PROClass The ProClass database is a non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies. PROClass De ProClass database er en ikke-redundante protein database organiseret efter familieforhold som defineret kollektivt af ProSite mønstre og Pir superfamilies. The ProClass database can facilitate protein family information retrieval, unveil domain and family relationships, and classify multi-domained proteins, by combining global and motif similarities into a single family organization scheme. De ProClass database kan lette protein familie oplysninger selektion, afsløre domæne og familieforhold, og klassificerer multi-domained proteiner, ved at kombinere global og motiv ligheder i en enkelt familie organisation ordningen.

ExPASY SWISS PROT Searchable index Molecular Biology Server of the University of Geneva: contains searchable index of SWISS-PROT. ExPASY SCHWEIZISKE PROT søgbart indeks Molekylær Biologi Server ved universitetet i Genève: indeholder søgbart indeks over schweizisk-PROT.

ExPASY PROSITE PROSITE is a database of protein families and domains. ExPASY PROSITE PROSITE er en database af protein familier og domæner. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. Den består af biologisk væsentlige steder, mønstre og profiler, der medvirker til at pålideligt identificere hvilken kendt protein familien (hvis nogen) en ny sekvens tilhører.

SYSTERS Protein Family Database by Motifs SYSTERS Protein Family Database ved Motifs

TIGRFAM Database are protein families based on Hidden Markov Models or HMMs. TIGRFAM databasen er protein familier baseret på skjulte Markov modeller eller HMMs.

eMotif Search The eMOTIFS are derived from the multiple sequence alignments in the BLOCKS+ database. eMotif Search eMOTIFS er afledt af de mange sekvens tilnaermelser i blokkene + database.

MOTIF : Can search multiple databases including: PROSITE Pattern, PROSITE Profile, BLOCKS, ProDom, PRINTS, Pfam, Pfam_fs for fragments, and a user-defined profile library. Motiv: Kan søge flere databaser herunder: PROSITE Mønster, PROSITE profil, blokke, ProDom, tryk, Pfam, Pfam_fs for fragmenter, og en bruger-defineret profil bibliotek.

HMM Search - Motif Search of a Protein Sequence using the Pfam-A Database of Protein Domains - Sanger Centre (UK). HMM Search - Motif ransagning af et protein Sequence bruge Pfam-en database over Protein Domains - Sanger Centre (UK).

HMM Search - Motif Search of a Protein Sequence using the Pfam-A Database of Protein Domains - WUSTL (US). HMM Search - Motif ransagning af et protein Sequence bruge Pfam-en database over Protein Domains - WUSTL (US).

MAST - Motif Alignment and Search Tool - Pasteur Inst (France). MAST - Motif Alignment og søgeværktøj - Pasteur Inst. (Frankrig).

MEME - Multiple EM for Motif Elicitation - Pasteur Institute (France). Tesen - Flere EM for Motif Elicitation - Pasteur Institute (Frankrig).

MOTIF - Pattern Search Service - Iowa State U (US) . Motiv - Mønster Search Service - Iowa State U (US).

PatternFind - Sequence Pattern Search- Pattern Search of several databases including: Swiss-Prot, TrEMBL, Swiss-Prot splice variants, trEST, trGEN, PatternFind - Sequence Mønster Search-Mønster Søg i flere databaser herunder: Swiss-Prot, TrEMBL, Swiss-Prot splejse varianter, trEST, trGEN,
trome, Current ENSEMBL peptides for all species, Microbial complete proteomes, RefSeq Release, RefSeq weekly updates, PATTINPROT - Query Sequence Pattern Search - Pole Bio-Informatique Lyonnaise (France), Pratt2.1 - Pattern Discovery Tool, Pratt - U Helsinki (Finland), Pratt - Pasteur Inst (France), Pratt - Inst Informatik-U Bergensis (Norway), Pratt - EBI (UK). trome, Current ENSEMBL peptider for alle arter, Mikrobiel komplet proteomes, RefSeq Release, RefSeq ugentlige opdateringer, PATTINPROT - Forespørgsel Sequence Mønster Search - Pole Bio-Informatique Lyonnaise (Frankrig), Pratt2.1 - Mønster Discovery Tool, Pratt - U Helsinki (Finland ), Pratt - Pasteur Inst. (Frankrig), Pratt - Inst. Informatik-U Bergensis (Norge), Pratt - EBI (UK).

PROSITE - Profile Motifs Searches of ProSite Database. PROSITE - Profil Motifs søgninger i ProSite Database.

PROSITE Search - Genestream - IGH Montpellier (France). PROSITE Search - Genestream - indvendige gearnav Montpellier (Frankrig).

ScanProsite - Scan a Protein Sequence against the PROSITE DB - ExPASy (Switzerland). ScanProsite - Scan et protein Sequence mod PROSITE DB - ExPASy (Schweiz).

Plant Protein Motif Databases: Vegetabilske proteiner Motif Databaser:

PlantP PlantP

PHYTOPROT The general procedure behind PHYTOPROT consists in performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences (Mohseni-Zadeh et al., Recomb 2003) based on their similarity and finally displaying à la Prodom the domains shared by the sequences in each cluster PHYTOPROT Den generelle procedure bag PHYTOPROT består i at udføre en "alt-for-alle" sammenligning af (putative) protein sekvenser med BIOFACET software, opbygning af klynger af sekvenser (Mohseni-Zadeh et al., Recomb 2003) baseret på deres lighed og endelig visning à la Prodom domænerne deles af sekvenser i hver klynge

Integr8 Arabidopsis Thalania Provides information about protein using keyword search. Integr8 Arabidopsis Thalania giver oplysninger om protein ved hjælp af søgeord søgning. Contains Domain information within the search. Indeholder Domæne information inden for søgning.

Pfam Arabidopsis Protein Families Pfam Arabidopsis Protein Familier

Parasite Protein Motif Databases: Parasite Protein Motif Databaser:

Parasite Motif Search Parasite Motif Database. Parasite Motif Search Parasite Motif Database. Databases of: All Leishmania, Leishmania major Friedlin, Trypanosoma brucei, Trypanosoma cruzi, All Crithidia, All kinetoplastids, Plasmodium falciparum, All Plasmodium, Toxoplasma gondii, All Apicomplexa, All Schistosoma, All Filarioidea. Databaser: Alle Leishmania, Leishmania store Friedlin, Trypanosoma brucei, Trypanosoma cruzi, Alle Crithidia, Alle kinetoplastids, Plasmodium falciparum, Alle Plasmodium, toxoplasma gondii, Alle Apicomplexa, Alle Schistosoma, Alle Filarioidea.

Other Species Protein Motif Databases: Andre arter Protein Motif Databaser:

Other Species at Integr8 Andre arter på Integr8

Pfam other species Pfam andre arter