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Kry proteïenaantekeninge van Uniprot uit proteïenkartering

Kry proteïenaantekeninge van Uniprot uit proteïenkartering


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Met 'n lêer van ongeveer 10k kartering identifiseerders, hoe kan ek die aantekeninge van die proteïene van Uniprot kry? Aangesien dit nie moontlik is om dit met die hand te doen nie

My kartering is vervat in 'n .csv-lêer Hulle is van STRING databasis Voorbeeld 9606.ENSP00000387699


Hierdie probleem word hier bespreek. Blykbaar is STRING ID's in KEGG-formaat, maar dit kan op Uniprot ID's gekarteer word deur inligting van hier af af te laai. Ek dink dit is óf die proteïen.aliasse data of die kartering_lêers data wat jy nodig het. Die eerste skakel verskaf 'n Python-skrip om nuttige inligting uit die afgelaaide data te onttrek. Dit is groot aflaaie so ek het dit nie eintlik self probeer nie.

Sodra jy die STRING→ Uniprot-omskakeling gedoen het, kan jy vermoedelik Uniprot navraag doen met die afvoer as 'n bondelversoek.

Sterkte!


UniProt se joernaal aflaai stelsel, voorgestel deur Alan Boyd hierbo, laat jou ook direk toe kaart identifiseerders, bv. STRING na UniProtKB, of Ensembl na UniProtKB: http://www.uniprot.org/uploadlists

Sodra jy jou UniProtKB-resultate het, kan jy kolomme byvoeg of verwyder deur op "Kolomme" te klik, en sodra jy gelukkig is, kan jy die resultate in oortjies-geskeide formaat aflaai (http://www.uniprot.org/help/customize ).


Kry proteïenaantekeninge van Uniprot uit proteïenkartering - Biologie

8 uur as gevolg van instandhouding in ons datasentrum. Hierdie interval kan moontlik korter wees, afhangende van die vordering van die werk. Ons vra om verskoning vir enige ongerief. *** --> *** DAVID sal af wees vanaf 17:00 EST Vrydag 24/6/2011 tot 15:00 EST Sondag 26/6/2011 as gevolg van instandhouding in ons datasentrum. Hierdie interval kan moontlik korter wees, afhangende van die vordering van die werk. Ons vra om verskoning vir enige ongerief. *** --> *** Ons aanvaar tans Beta-gebruikers vir ons nuwe DAVID-webdiens wat toegang tot DAVID vanaf verskeie programmeertale moontlik maak. Kontak ons ​​asseblief vir toegang. *** --> *** Die genesimbool-kartering vir lysoplaai en omskakeling het verander. Sien asseblief die DAVID-forumaankondiging vir besonderhede. --> *** Die aankondiging van die nuwe DAVID Webdiens wat toegang tot DAVID vanaf verskeie programmeertale moontlik maak. Meer inligting. *** --> *** DAVID 6.8 sal af wees vir instandhouding op Donderdag, 23/2/2016, vanaf 09:00-13:00 EST *** -->
*** Welkom by DAVID 6.8 ***
*** As jy op soek is na DAVID 6.7, besoek asseblief ons ontwikkelingswerf. ***
-->
*** Welkom by DAVID 6.8 met opgedateerde kennisbasis (meer inligting). ***
*** As jy op soek is na DAVID 6.7, besoek asseblief ons ontwikkelingswebwerf. ***
-->
*** Welkom by DAVID 6.8 met opgedateerde kennisbasis (meer inligting). ***
*** Die DAVID 6.7-bediener is tans af vir onderhoud. ***
--> *** Lees asseblief: As gevolg van instandhouding van datasentrums, sal DAVID van Vrydag 17 Junie @ 16:00 EST tot Sondag 19 Junie vanlyn wees met die moontlikheid om gouer weer aanlyn te wees. *** -->


Aanbieding Transkripsie

Proteïen inligtingsbron Toesig- en Wetenskaplike Adviesraad Vergadering 14 November 2005 Georgetown Universiteit Mediese Sentrum

Welkom en inleiding Vassilios Papadopoulos, Ph.D. Mede-visepresident en direkteur, Biomediese Nagraadse Navorsingsorganisasie Georgetown Universiteit Mediese Sentrum David State, M.D., Ph.D. Voorsitter, PIR Toesighoudende en Wetenskaplike Adviesraad Professor en Direkteur van Bioinformatika, Universiteit van Michigan

PIR/UniProt OorsigProjek Oorsig, Organisasie, Infrastruktuur Cathy H. Wu, Ph.D. Direkteur, PIR Professor, Georgetown Universiteit Mediese Sentrum

Proteïeninligtingsbron (PIR) Geïntegreerde proteïeninformatikahulpbron vir genomiese/proteomiese navorsing • UniProt universele proteïenhulpbron:Sentrale hulpbron van proteïenvolgorde en -funksie • PIRSF-familieklassifikasiestelsel: proteïenklassifikasie en funksionele annotasie • iProClass-geïntegreerde proteïendatabasis: data-integrasie en proteïenkartering • Kuberinfrastruktuur (interoperabiliteit en Verspreiding): Ontologie, XML, Object/Relasionele DB, J2EE Architecture http://pir.georgetown.edu

UniProt: Universele Proteïenhulpbron Sentrale Hulpbron van Proteïenvolgorde en -funksie • Internasionale Konsortium • Proteïeninligtingshulpbron (PIR) • Europese Bioinformatika Instituut (EBI) • Switserse Instituut vir Bioinformatika (SIB) • NIH U01-toekenning (NHGRI/NIGMS/NLM/NIMH/NCRR/NIDCR) • Fase I (09/02-08/05): $6 miljoen jaarliks ​​• Brug (09/05-?/06): $6.6M • Fase II (?/06-?/09): $6.6-8.0(?)M http ://www.uniprot.org NHGRI

UniProt Argief (UniParc) Omvattende volgorde-argief met volgordegeskiedenis Geproduseer by EBI UniProt Reference Clusters (UniRef) Nie-oortollige verwysingsklusters vir volgordesoektog Geproduseer by PIR UniProt Knowledgebase (UniProtKB) Integrasie van PIR-PSD, Swiss-Prot en TrEMBL databasisse Stabiele, omvattende, volledig geklassifiseerde, ryk en akkuraat geannoteerde kennisbasis UniProtKB/Swiss-Prot: Geproduseer by SIB UniProtKB/TrEMBL: Geproduseer by EBI Literatuurgebaseerde en outomatiese annotasie by SIB, PIR, EBI UniProt-databasisse

UniProt Bestuurstruktuur • Wetenskaplike Adviespaneel (SAP) sal deur NHGRI ingestel word

UniProt-projekkoördinering • UniProt-e-posbesprekingsgroepe • Projekskakeling en ad hoc-spanne • Drieweeklikse telekonferensie-oproepe • Driejaarlikse aangesig-tot-aangesig-konsortiumvergaderings • 12-13 Januarie 2006 in Genève • 10-11 April 2006 by Georgetown Universiteit • Uitruil besoeke van wetenskaplike en tegniese personeel • Vyf PIR-personeel by SIB (1-2 weke, 5 Nov) vir annotasie-integrasie • Retreats Frankryk, 2004

UniProt-aktiwiteite by PIR • Integrasie van PIR-PSD in UniProtKB Swiss-Prot/TrEMBL • Inkorporering van unieke PIR-inskrywings • Inkorporering van PIR-aantekeninge: verwysings, eksperimentele kenmerke met literatuurbewysmerker • Funksionele annotasie van UniProtKB-proteïene • Ontwikkeling van PIRSF-familieklassifikasiestelsel en PIRSF-kurasie = > Omvattende dekking van alle UniProtKB-proteïene • Ontwikkeling van reël-gebaseerde annotasiestelsel & PIRNR (naamreël) /PIRSR (werfreël) kurasie => Reël kurasie en integrasie in Swiss-Prot/TrEMBL annotasie pyplyne & voortplanting van annotasies (bv. naam , GO, werf) • Produksie van UniRef100/90/50 databasisse =>Verbetering &skalering • Skep van UniProt webwerf en hulpstelsel => Unified UniProt webwerf & gebruiker gemeenskap interaksie

PIRSF Klassifikasiestelsel Proteïenklassifikasie en funksionele annotasie • PIRSF: Evolusionêre verwantskappe van proteïene van super- tot subfamilies • Gekureerde families met naamreëls en terreinreëls • Kurasieplatform met klassifikasie/visualiseringsinstrumente • Aflewerbares: UniProtKB-aantekeninge, InterPro-families, PIRSF-verslae, PIRSF-kurasie platform PIRSF Werkgroepvergadering, April 2003

iProClass-geïntegreerde proteïendatabasis Data-integrasie en proteïenkartering • Data-integrasie vanaf >90-databasisse • ​​Onderliggende datapakhuis vir proteïen-ID/naam/bibliografie-kartering • Integrasie van proteïenfamilie, funksie, struktuur vir funksionele annotasie • Ryk skakel (skakel + opsomming) vir waardetoegevoegde verslae van UniProt proteïene Befonds deur NSF

iProLINK Literatuur Mynbouhulpbron • Bibliografieverslag: geannoteerde bibliografie vir UniProtKB-proteïene • BioThesaurus-verslae: Proteïen- en geenname vir UniProtKB-proteïene • RLIMS-P-program: Tag PubMed-abstrakte vir fosforileringsvoorwerpe • Proteïenontologie DAG: PIRSF-gebaseerde ontologie Befonds deur NSF

NIAID Proteomiese Admin Sentrum • NIAID Proteomic Master Catalog & Complete Proteomes • iProXpress vir proteïenfunksie en roete-analise • Geen/peptied-proteïen-kartering • sekwensie-analise en amp data-ontginning • Funksie/ Pathway Discovery http://pir.georgetown.edu/ proteomics/ Befonds deur NIAID

Bioinformatika-infrastruktuur • NCI caBIG: PIR-roosteraktivering (Programmering toegang tot UniProtKB) • NSF TeraGrid: Alles-teen-almal BLAST (UniProtKB-verwante reekse) • PIR Bioinformatika-raamwerk • Sagtewareraamwerk: J2EE n-vlakargitektuur met objekmodelle • Databasisverspreiding: XML , FASTA, Relasioneel (Oracle 9i, MySQL) • Ander aflewerings: objekmodelle, webdienste wat deur NCI befonds word

Rekenaaromgewing • Rekenaars: Two Sun V880, IBM P690, 100-CPU Linux Cluster, Compaq 4100 Alpha • Netwerk: Internet2, GU Network (1Gbps) • GU UIS Advanced Research Computing

$3Miljoen Jaarlikse Totaal (2/3 UniProt, 1/3 Ander) • Tuisinstelling: Georgetown Universiteit Mediese Sentrum (GUMC) • Subkontrak: Nasionale Biomediese Navorsingstigting (NBRF) • Nuwe ligging: Buitekampus (GU Noordkampus), 6250 SQFT Suite 1200, 3300 Whitehaven Street NW, Washington, DC 20007

PIR organisasie • 25 personeellede • 14 GU, 11 NBRF • 22 VE's • 12,7 GU, 9,3 NBRF • 17 met doktorsgraad • 11 GU-fakulteit • 2 professore • 1 navorsingsmedeprofessor • 6 navorsingsassistent-professore • 2 navorsingsinstrukteurs

PIR-gemeenskapsinteraksies (sedert 2004) • Aanbiedings en genooide seminare • NIH Proteomics-werkswinkel (Tweejaarliks) – Bioinformatikadag • Konferensiedemo's/plakkate: ISMB-05, US HUPO-05, SOFG04 • Meer as 20 Genooide aanbiedings: Keystone, Human Brain Project Satellite Simposium, PDB Simposium, HUPO-05 • Beleidsforums, Komitees: NSF Plant Cyberinfrastructure, NIH Protein Structure Initiative, HUPO Proteomics Standards Initiative • Publikasies: Meer as 25 gekeurde referate en boekhoofstukke • Samewerkings en interaksies • Samewerking en interaksie gehad met meer as 10 navorsingsinstellings • Gehuisves van aangesig tot -gesigvergaderings vir NIAID/caBIG-projekte • Referaat- en Grant-resensies • Beoordeel meer as 20 referate vir verwysde joernale en konferensies • Gedien op NSF/NIH-toekenningsoorsigpanele

PIR-Georgetown Interaksies • Onderrig • Kursusse: Bioinformatika (BCHB 521), Gevorderde Bioinformatika (BCHB 621) • Lesings: Mediese Biochemie, Proteïenbiomerker, Inleidende Biologie • Mentorskap • Begelei 9 nagraadse studente (PhD-studente, MS-internskapprojekte) • Interkampus Seminare deur • Voorleggingsvoorlegging deur PIR Jong Ondersoekers as PI • Ses voorstelle aan federale en ander agentskappe

PIR/UniProt – Opsomming en statistieke Databasisgroei Databasisgebruik Unified UniProt Webwerf PIR UniProt Consortium Interaksies Peter McGarvey, Ph.D.

Kliënt-e-pos [email protected] & [email protected] 550 UniProt-e-posse 720 PIR-e-posse 1 Dag Omkeer “PIR is 'n wonderlike hulpbron.” – Craig “Dankie vir jou vinnige reaksie, soos altyd is UniProt op die spel!” – Fiona

PIR/UniProt – Unified UniProt Webwerf • 3 Desember, Drie gesinchroniseerde werwe gebaseer op PIR-ontwerp • 4 Nov., Gevestigde doelwitte vir verenigde webwerwe. • 2005, Back-end Data en Sagteware Platform Ontwikkel. • 5 November, PIR speel 'n hoofrol in die ontwikkeling van spesifikasies vir die koppelvlak. • 6 Junie, vrystelling van verenigde UniProt-webwerf wat deur PIR en EBI aangebied word

PIR/UniProt - Konsortium-interaksies • UniProt-skakelgroep (bespreking van hoëvlakkwessies) • UniProt-webwerfkomitee (Unified UniProt-webwerfbeplanning) • UniProt-skakelkomitee (werk met eksterne databasisse) • UniProt-hulppos (beantwoord gebruikersnavrae) • UniProt-dokumentkomitee (dokumentasie) , tutoriale en Gereelde Vrae) • UniProt XML-groep (XML-dokumentasie en instandhouding) • UniProt-groep vir outomatiese annotasie-pyplyn • Handmatige samestelling van Swiss-Prot-sjabloonreekse • Handmatige samestelling van terreinreëls en beheerde woordeskat • Ontwikkeling van outomatiese aantekeningreëls • Ontwikkeling van proteïen benoemingsriglyne • Inkorporering van nuwe proteïenfamilies by InterPro • PIR besoek gereeld kollegas van EBI en SIB of huisves vir besprekings. • Tweeweeklikse opdatering van UniRef, UniParc en UniProtKB databasisse

Proteïenklassifikasie en annotasie Darren Natale, Ph.D. Spanleier, Proteïenwetenskap, PIR Navorsingsassistent, GUMC

Proteïenkurasieaktiwiteite • PIRSF – klassifikasie van homeomorfiese proteïene gebaseer op evolusionêre verwantskappe • PIRNR – familie-gebaseerde “Naamreëls” wat die parameters definieer vir die voortplanting van spesifieke naam, EC en GO-aantekening aan lede • PIRSR – familie-gebaseerde “Site Reëls” wat die parameters definieer vir die verspreiding van spesifieke kenmerkaantekeninge aan lede

Gespesialiseerde gereedskap (I) • Pfam/PIRSF-hiërargie • Domeinverwante • Domeinsamestelling DAG Behou hierdie drie kenmerke in 'n navigeerbare formaat In redigeermodus, laat maklike skepping, vernietiging en beweging van PIRSF's toe

Gespesialiseerde gereedskap (II) HPS KGPDC Filogenetiese Boom Klassifikasie/Annotasie Belyning PIR Tree and Alignment Viewer (PIRTAV) HPS = 3-heksulose-6-fosfaat sintase KGPDC = 3-keto-L-gulonaat 6-fosfaat dekarboksilase

PIRSF Curation Pipeline • On-gekureerde vlak – rekenaargegenereerde • Voorlopige kurasievlak • Kuratelidmaatskap (beginselnutsmiddels: BLAST-resultate, iteratiewe ontploffingsgroep, on-the-fly HMM) • Kurateer domeinargitektuur • Kies sade • Volledige kurasievlak • Kuratornaam en sommige verwysings • Opsioneel : skryf abstrak wat funksie, struktuur, ens aandui. (Slegs volle vlak) Na naamhersieningsessie en HMM-prestasiekontrole, word alle inligting (HMM, lidmaatskap, annotasie) na EBI gestuur vir integrasie in InterPro.

PIRNR Kurasie Pyplyn • Begin met PIRSF saamgestel na Volle vlak • Definieer pasmaatstawwe vir toepassing van die reël • Hersien proteïennaam, sinonieme, EC-nommers, GO-terme • Soek dié wat toepaslik is om te versprei aan lede wat ooreenstem met reëlkriteria Na hersiening van verspreibare inligting, stuur pas voorwaardes, uitsluitingsvoorwaardes en gepropageerde velde by EBI vir insluiting in outomatiese annotasie-pyplyn. Resultate word in EBI se UniProt-inskrywing uitgebreide aansig vertoon.

PIRSR Kurasie Pyplyn • Begin met PIRSF met saamgestelde lidmaatskap en sade. Ten minste een lid moet struktuur opgelos het. • Redigeer saad-tot-struktuur-belyning om geconserveerde streke te definieer en te behou wat pertinente oorblyfsels dek • Bou Site HMM van aaneengeskakelde geconserveerde streke • Definieer kenmerkaantekening deur gebruik te maak van beheerde woordeskat met bewystoeskrywing Pas reëls toe op PIRSF-lede, skep loglêers om na SIB (UniProtKB) te stuur /Swiss-Prot) of EBI (UniProtKB/TrEMBL). Resultate word in UniProtKB plat lêers opgeneem.

Vordering met proteïenkurasieaktiwiteite 1207 1001 83 428DE/GO/EC 342DE/GO 157DE 561 420 251 112 38 14 162 Voorlopig 693 Vol 352 Vol + Desc 35 Aktief 34 Metaal/Bind 14 Misc. 4222 1595 1266

Impakmetings • PIRSF's geïntegreer in InterPro • Gestuur: • PIRSF-uniek: • PIRNR raak UniProtKB/TrEMBL • Inskrywings: • Aantekeningreëls: • PIRSR raak UniProtKB • Inskrywings: • Kenmerklyne: 1,775 840 60,300 281,400,000,000 7,0000,000,000,000 7,000 )

Verhoogde deurset en impak Samegestel met Struktuur Vol Aktief + Ligand na InterPro AutoAnno Aktief Verhoogde spesifisiteit PIRSF PIRNR PIRSR • Beklemtoon Full/InterPro • Reëls vir EBI • Aktiewe terreine • Omvattende dekking • Kurasie “stoot” • Voortplanting by PIR • Voeg ligand-binding by Al drie sal geïntegreer word in die Swiss-Prot annotasie platform Al drie sal geïntegreer word in die Swiss-Prot annotasie platform Al drie sal geïntegreer word in die Swiss-Prot annotasie platform

UniRef-databasisse Hongzhan Huang, Ph.D. Bioinformatika-spanleier Proteïeninligtingshulpbron, GUMC

UniRef (UniProt Reference Clusters) • Nie-oortollige verwysingsklusters vir volgordesoektogte • Afgelei van UniProtKB en geselekteerde UniParc-bronne • UniRef100: 100% volgorde-identiteit • UniRef90: 90% volgorde-identiteit (1/3 grootte vermindering vanaf UniRef100) • UniRef50: (50/% volgorde-identiteit) 3 grootte vermindering) Vrystelling 6.4 (5 Nov.)

Sub-fragmente UniRef100 • Die mees omvattende reeksdatastel vir volgordeooreenkomstesoektog • 3,176K rye in UniRef100 vs. 3,022K reekse in NCBI nr • Bronreekse • Voltooi UniProtKB - Splitsvariante as aparte inskrywings • Geselekteerde UniParc (bv. Ensembl) en No Ref-Seq. • Kombineer identiese rye van alle spesies • Voeg subfragmente saam

UniRef90 & UniRef50 • Verminderde volgorde datastelle vir vinniger volgorde ooreenkoms soek • Verteenwoordigende volgorde vir elke groepering • Groepering Algoritme • CD-HIT: Vinnig, bo-na onder, nie-oorvleuelend • PIR se parallelle weergawe wat op Linux Cluster UniRef90: 1/3 grootte verkleining UniRef50: 2/ 3 grootte verkleining

UniRef50-volgordeklassifikasie • Heeltemal outomatiese, tweeweekliks bygewerkte klassifikasie van alle proteïene • Hoe goed is die UniRef50-klusters? • Geëvalueer deur alles-teen-almal BLAST-soekresultate • 98% van die trosse is van goeie gehalte: elke ry pas by elke ander rye binne die groep • Problematiese trosse • ​​Een lang ry oorbrug twee of meer nie-verwante subgroepe. • Kan die gevolg wees van verkeerde geenmodelle, domeinsamesmelting, poliproteïen • Nuwe algoritme sal ontwikkel word met lengte/oorvleueling parameters om sulke trosse op te spoor en te hergroepeer.

PIRCF-gesinne (Rekenaar-gegenereerde gesinne) UniRef50-klusters PIRSF-gesinne Voeg verwante groepe saam Gekontroleer deur kurator Gebruike van UniRef-klusters • UniRef90/50 vir omvattende outomatiese klassifikasie van proteïene • Vinniger soektogte en minder deurmekaar ooreenkomssoektog-uitsette • Meer egalige steekproefneming van volgorderuimte en vermindering van soektog vooroordeel • UniRef vir integriteitkontrolering van databasisannotasie • Uniref100 om EST-volgordes te annoteer • UniRef50 om verkeerde geenmodelle op te spoor • UniRef90/50 vir PIRSF-familieklassifikasie • UniRef90 om nuwe PIRSF-familielede te werf • UniRef50 om nuwe PIRSF-families te skep

Letterkunde Mynbou Zhang-Zhi Hu, M.D. Mede-spanleier, Proteïenwetenskap, PIR Navorsingsassistent Professor, GUMC

Voltooi UniProtKB bibliografie kartering RLIMS-P-teksmyninstrument vir proteïenfosforilering BioThesaurus: proteïen-/geenname iProLINK 'n Geïntegreerde hulpbron vir proteïenliteratuurontginning

PIR/UniProt Proteïen Bibliografie • 355 629 unieke aanhalings (PMID) is in iProClass vir 2,4 miljoen UniProtKB-inskrywings. • 166 950(47%)aanhalings is tans in UniProtKB. • Die bykomende 188 679 (53%) unieke aanhalings is geneem uit bronne soos GeneRIF, SGD, MGI. Bibliografieverslag: • saamgestelde aanhalings • gebruiker ingedien • rekenaarmatig gekarteer

BioThesaurus verslag BioThesaurus – omvattende versameling geen-/proteïenname uit verskeie bronne en hul assosiasies met databasis-entiteite. Toepassings van BioThesaurus • Geen/proteïenname kartering • Soek sinonieme • Los naamdubbelsinnigheid op • Databasisaantekening • Foutbespeuring: botsende name in UniProtKB • Literatuurontginning • Navraaguitbreiding: sinonieme en teksvariante maak voorsiening vir uitgebreide soekresultate IAPP IAPP genoem in 18 inskrywings

kinase substraatwerwe PMID-kartering Reëlgebaseerde LIteratuur-mynstelsel vir proteïenfosforilering RLIMS-P – RLIMS-P-verslag – PMID:1939059 MEDLINE abstrak (PubMed ID) P12957 RLIMS-P Fosforileringskenmerk-onttrekking UniProtKB-inskrywingskaartering is tans 18K207B entphosphortasie met 18K207B entry-kartering. . • 105Kunique-aanhalings (PMID) is in UniProtKB/Swiss-Prot • Bondelverwerking deur RLIMS-P het 4690 opsommings met fosforileringsinligting opgelewer, 913 van hulle met werfinligting, insluitend 214in UniProtKB-inskrywings met geen geannoteerde fosforilering-kenmerke. UniProtKB webwerf kenmerk annotasie en bewyse toeskrywing

NIAID Biodefense Proteomics Program • 7 Proteomika-navorsingsentrums: Identifisering van teikens vir terapeutiese intervensies “.. ontdek teikens vir potensiële kandidate vir die volgende generasie van entstowwe, terapeutika en diagnostiek” • Administratiewe Hulpbronsentrum: Ondersteun navorsingsentrums, publieke verspreiding van resultate en protokolle ..vestig 'n Wetenskaplike werkgroep, interoperabiliteitswerkgroep, data-infrastruktuur en bevorder bewustheid van die projek sodat wetenskaplikes wêreldwyd hierdie hulpbronne kan benut.

Administratiewe hulpbron • Projekbestuur - Sosiale & Wetenskaplike Stelsels (SSS) • Vergaderings en Kommunikasie • Webportaal • NIAID Jaarvergadering by PIR Mei 2006 • Wetenskaplike Koördinering - PIR & VBI • Wetenskaplike Advieswerkgroep (SWG) • Interoperabiliteitswerkgroep (IWG) • Data Infrastruktuur – PIR & VBI • Proteomiese databasis: berging en herwinning (VBI) • Databestuur- en analisenutsmiddels (PIR/VBI) • Geïntegreerde proteïenkennisstelsel (PIR)


2 STELSELS EN METODES

2.1 Proteïenvolgordes

Proteïene wat 'n gespesifiseerde eukariotiese transkripsiefaktordomein bevat is gevind in die NCBI nie-oortollige databasis, 24 April 2004 uitgawe (Benson et al., 2004): 1255 basiese leucine rits proteïene (bzip), 1379 kern reseptor proteïene (nr) en 592 drie C2H2 sink vinger proteïene (3zf). Vir beide C2H2 sinkvinger en basiese leucine ritsen, 'n PROSITE konsensus matriks ( Hulo et al., 2004) is deur die pfscan-program (Bucher et al., 1996) om die databasis te deursoek deur die verstekparameters te gebruik. Hierdie konsensusmatrikse word onderskeidelik deur toegangsnommers PS50157 en PS50217 gemerk. Vir die kernreseptordomein, 'n PROSITE-konsensuspatroon (Hulo et al., 2004), toegangsnommer PS00031, is gebruik deur 'n Perl-program wat ons ontwikkel het om die databasis te deursoek. Hierdie patroon is uitgebrei na 102 aminosure om die C-terminale uitbreiding van die domein in te sluit.

C2H2 sinkvingerpatrone is individueel gevind. Proteïene is by hierdie studie ingesluit as hulle drie C2H2-sinkvingers in 'n 106 aminosuurreeks bevat het en as geen ander C2H2-sinkvingers, selfs swak pasmaats, in die proteïen gevind is nie. C2H2 sinkvingerproteïene met drie opeenvolgende vingers is gekies omdat dit een van die belangrikste groeperings van C2H2 sinkvingerproteïene is (Iuchi, 2001) en ook voorsiening maak vir 'n konsekwente domeingrootte.

Slegs die opeenvolging wat deur die soekalgoritme gevind is, is in die analise gebruik omdat dit die domeine is wat direk by proteïen-DNS-interaksies betrokke is. Die gebruik van slegs subsekwensies beperk ook moontlike verwarring wat kan ontstaan ​​in hele proteïenbelynings van domeinoordrag en herrangskikkingsgebeure (Liu en Rost, 2003).

2.2 Bindende spesifisiteite

Bindende spesifisiteite is gevind deur 'n uitgebreide literatuursoektog. Spesifisiteitsbepalings is slegs aanvaar indien die eksperimentele metodes ten minste 'n affiniteit vir die voorgestelde bindingsplek bevestig het. Proteïene gemerk as ortoloë in SWISSPROT ( Apweiler et al., 2004), soos muis- en menslike weergawes van c-JUN, is aanvaar om identiese bindingspesifisiteite te hê. Omdat hierdie proteïene as ortoloë 'n gedetailleerde vlak van funksie behoort te deel, neem ons aan dat hulle eweneens die intermediêre funksievlak sal deel.

Ons sou verkies het om ook die verskillende konsensus DNA-bindende volgordes te groepeer en so die funksies op dieselfde manier as die rye te groepeer. Konsensusreekse word egter op 'n verskeidenheid maniere gerapporteer. Hulle verskil in die lengte van die voorspelde volgorde en die hoeveelheid variasie in basisreekse wat toegelaat word. Om hierdie rede kon ons nie die DNS-volgordes op 'n sinvolle manier groepeer nie. Vir hierdie werk het ons die DNS-volgordes met die hand gegroepeer en probeer om so na as moontlik die mening van die eksperimentele gemeenskap te pas. Om op hierdie manier met die beskikbare bewyse te vergelyk, sal 'n sinvolle toets van ons resultate bied.

Die soektog het gelei tot 11 verskillende bindingspesifisiteite vir 144 bzip-proteïene, 4 verskillende spesifisiteite vir 209 nr-proteïene en 7 verskillende spesifisiteite vir 53 3zf-proteïene. Dit stem ooreen met 11,5, 15,2 en 9,0% van proteïenvolgordes in die onderskeie transkripsiefaktorfamilies. Bindende spesifisiteite wat in hierdie studie gebruik is, is beskikbaar in die aanvullende materiaal. Die persentasies proteïene met bindingspesifisiteite in die trosse word in Aanvullende Tabelle 6-9 gerapporteer.

2.3 Reeksvergelyking

'n Spesifieke tipe volgorde-ooreenkoms, volgorde-identiteit, word gedefinieer as die aantal aminosuurresidu-posisies in 'n paarsgewyse belyning gedeel deur die lengte van moontlike ooreenstemmende posisies. Soos Tian en Skolnick (2003), vind ons dat 'globale' volgorde-identiteit die beste definisie gee. 'Globale' volgorde-identiteit word gedefinieer as die aantal identiese residue gedeel deur die totale lengte van die belyning. Volgorde-identiteit is bepaal deur gebruik te maak van die align0-program in die FASTA-pakket (Pearson en Lipman, 1988).

Die rybelynings sal betroubaar wees omdat die rye in die grafiek 'n hoë mate van volgorde-identiteit deel. Daar is gevind dat volgordebelynings tussen rye met die vlak van identiteit onder 25% dikwels onakkuraat is (Thompson et al., 1999). Die hoë vlak van volgorde-identiteit vind plaas omdat ons slegs homoloë DNA-bindende domeine in elke grafiek vergelyk.

Ander maatstawwe van ooreenkoms soos paarsgewys BLAST-verwagtingswaardes (E-waardes) ( Altschul et al., 1990) gee soortgelyke resultate, maar volgorde-identiteit is gekies vanweë die eenvoud van definisie. Wanneer BLAST (blastall weergawe 2.2.9) gebruik word, is die gemiddelde paarsgewyse logboek E-waarde is gebruik, na die voorbeeld van Enright et al. (2002).

2.4 Groeperingsmetodes

Ons gebruik enkelskakelgroepering vanweë die eenvoud daarvan. In hierdie metode word 'n volgorde-ooreenkoms-afsnywaarde gekies en enige verbindings met ooreenkomswaardes onder hierdie afsnywaarde word verwyder. Proteïene wat steeds verbind is, selfs indirek, word as deel van dieselfde groep beskou. Ons beskou alle volgorde-identiteit-afsnywaardes van 0 tot 1.

Een van die mees gesofistikeerde ander metodes om proteïene op 'n grafiek te groepeer is TRIBE-MCL (Enright et al., 2002). Hierdie metode gebruik die Markov cluster (MCL) algoritme van Van Dongen (Enright et al., 2002 Van Dongen, 2000). Die algoritme gebruik 'n grafiek waar die ongerigte rande die log van die gemiddelde paarsgewyse BLAST bevat E-waardes. Dit verander hierdie E-waardes in waarskynlikhede van oorgange tussen nodusse tydens 'n ewekansige stap, en bereken dan die waarskynlikhede om verskillende paaie te kies. Iteratiewe 'inflasie' en 'uitbreiding' bewerkings op die matriks van waarskynlikhede skei die grafiek in verskillende trosse deur die waarskynlikheid van stappe binne 'n groep te verhoog en die waarskynlikheid om tussen trosse te beweeg, te verminder. 'n Parameter wat tydens die 'inflasie'-operasie gebruik word, die inflasieparameter, word hoofsaaklik gebruik om die korreligheid van die grafiek te beïnvloed.

Vir die kernreseptorfamilie van proteïene gee die TRIBE-MCL-algoritme slegs 'n volledig gekoppelde grafiek in die hele reeks van die inflasieparameter (van 1.01 tot 5). Om die algoritme op verskillende vlakke van granulariteit te toets, moes ons hierdie groot groep kan skei. Die MCL webwerf FAQ bied 'n bykomende manier om die grafieke fyner te maak in Afdeling 5.3 (http://micans.org/mcl/man/mclfaq.html#faq5.3). Ons het die voorbeeld gevolg en 'n parameter van 3.0 gebruik. TRIBE-MCL was toe in staat om die proteïene teen verskillende korrels te skei. Dit is die TRIBE-MCL resultate wat vir die kernreseptorfamilie aangebied word.

2.5 Visualisering

'n Subset van die proteïene in die grafiek word visueel getoon met elke nodus gekleur deur sy eksperimenteel bepaalde DNS-spesifisiteit. Proteïene is geselekteer vir visualisering van die trosse as hulle van mense afkomstig is en bekende bindingspesifisiteite gehad het. Menslike proteïene is gekies as gevolg van die groot hoeveelheid eksperimentele werk wat aan hierdie proteïene of aan die proteïene van naverwante organismes gewy is.

In sulke visualiserings dui stippellyne trosse aan wat in die grafiek gekombineer is deur ander rye as dié wat vertoon word. Hierdie stippellyne dui slegs aan dat die trosse gekombineer is en is nie bedoel om die werklike aanhegtingspunte te wys nie. Die aantal menslike proteïene met bindingsdata in elke groepie kan in Aanvullende Tabelle 6–9 gevind word.

Afsonderlike visualiserings is ook gemaak vir die TRIBE-MCL resultate. Die uitvoer van die algoritme lys slegs die groep waaraan elke proteïen behoort. Rande is tussen proteïene in dieselfde groep bygevoeg om die TRIBE-MCL resultate op 'n soortgelyke wyse as die resultate van ons metode te vertoon. Die program Graphviz (Gansner en North, 2000) is gebruik om al die visualiserings te vertoon.

2.6 Puntetelling

Ons het die volgende matriksmetode gebruik om die telling te kwantifiseer. Vir 'n grafiek van N totale proteïene met M. proteïene met 'n bekende bindingspesifisiteit, an M. × M. laer driehoekige matriks, wat die verbindingsmatriks genoem word, is geskep. Ons gebruik 'n laer driehoekige matriks omdat die volle matriks simmetries is. As nodusse ek en j is in dieselfde groep, die waarde by posisie ij van die matriks is 1. As die nodusse nie in dieselfde groep is nie, is die waarde 0.

Ons het eweneens 'n M. × M. laer driehoekige matriks van die DNA-bindende spesifisiteite, genoem die DNA-bindende matriks. As twee proteïene ek en j eksperimenteel bepaal is om dieselfde of baie soortgelyke DNS-volgordes te bind, is die waarde weer 1, en dit is 0, anders.

Die twee matrikse is toe afgetrek: die konnektiwiteitsmatriks minus die DNA-bindende matriks. 'n Waarde van +1 beteken dat daar 'n vals positief is. 'n Waarde van −1 beteken dat daar 'n vals negatief is. 'n Waarde van 0 waar die posisie 1 in beide die matrikse is, dui op 'n ware positief anders, 'n waarde van 0 stem ooreen met 'n ware negatief. Die telling word gegee deur die aantal ware positiewes oor die som van die aantal ware positiewe, vals positiewe en vals negatiewe.

2.7 Gerandomiseerde spesifisiteite

Om die belangrikheid van die tellings te toets, is tellings bereken wanneer die bindingspesifisiteite ewekansig onder die M. proteïene met bekende eksperimentele data. Dieselfde getalle proteïene pas by 'n gegewe DNS-bindingspesifisiteit voor en na ewekansigheid. Vir elke telling is 1000 ewekansige DNS-bindende matrikse geskep en gebruik om ewekansige tellings te bereken. Hierdie waardes is dan gebruik om 'n gemiddelde en standaardafwyking te bereken. Afstande van die ware telling vanaf die ewekansige gemiddelde telling is dan gekwantifiseer as 'n Z-telling, die verskil in eenhede van die standaardafwyking.

2.8 Filogenetiese verwantskappe

As deel van die ontleding van die resultate, CLUSTALW ( Thompson et al., 1994) is gebruik om benaderde filogenetiese verwantskappe tussen die proteïene met 'n gegewe domein te bepaal. Phylip (Felsenstein, 1989), weergawe 3.6, is gebruik om 'n ongewortelde geenboom met behulp van hierdie verwantskappe te plot.


Abstrak

'n Gebrek aan die volledige varkproteoom het 'n gaping in ons kennis van die varkgenoom gelaat en het die haalbaarheid van die gebruik van varke as 'n biomediese model beperk. Ons het die weefselgebaseerde proteoomkaart ontwikkel deur 34 hoof normale varkweefsels te gebruik. 'n Totaal van 5841 onbekende proteïen isovorme is geïdentifiseer en sistematies gekarakteriseer, insluitend 2225 nuwe proteïen isovorme, 669 proteïen isovorme van 460 gene gesimboliseer begin met LOC, en 2947 proteïen isovorme sonder duidelike NCBI annotasie in huidige vark verwysing genoom. Hierdie nuut geïdentifiseerde proteïen-isovorme is funksioneel geannoteer deur die profilering van die vark-transkripsie met hoë-deurset RNA-volgordebepaling van dieselfde varkweefsels, wat die genoomannotasie van die ooreenstemmende proteïenkoderende gene verder verbeter het. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellular components and potential function for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.75% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.


Molecular Biology Freeware for Windows

A good places to start is Genamics SoftwareSeek. The following sites are arranged in the order that I discovered them. At some point they will be clustered by poreference:

DNA, RNA and genomic analysis:

Gegenees is a software project for comparative analysis of whole genome sequence data and other Next Generation Sequence (NGS) data. The software can e.g. compare a large number of microbial genomes, give phylogenomic overviews and define genomic signatures unique for specified target groups. I have been using this software which permits BLASTN and TBLASTX comparisons on phage sequences in order to define relationships ( Reference: Agren J et al. 2012. PLoS One. 7:e39107)

MyRAST - It is now possible to get a fairly accurate annotation of a prokaryotic genome in about a day using this software package. The latest Windows or Mac version of the software can be downloaded from here . You should check out the help page - Annotating a Genome Using myRAST and Distribution of the SEED server packages

Tablet - Next Generation Sequence Assembly Visualization - is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. File format support for ACE, AFG, MAQ, SOAP2, SAM and BAM. Import GFF3 features and quickly find/highlight/display them. Search and locate reads by name across entire data sets. Entire-contig overviews, showing data layout or coverage information.

BlastStation-Free supports megablast, blastn, blastp, and blastx searches allows easy database creation from your FASTA or FASTQ file, which can be compressed in .gz, .Z, or .zip format. A graphical display of search results and a summary table display of search results. The latter can be exported in CSV format, while the hit sequences can be exported in FASTA format. Also available for download in Mac or PC format.

Gene Designer- a brilliant software tools that allows one to combine building blocks such as regulatory DNA elements (promoters, ribosome-binding sites) with amino acid sequences, affinity & protease cleave tags and cloning features and codon optimize for any expression host.

CLC Free Workbench - allows basic sequence analysis such as open reading frame determination, restriction site analysis, translation from DNA/ RNA to proteins, alignments, and tree reconstruction in a single window format.

EMBOSS (European M.oliekulêr Biology Open Source Software Suite) can be downloaded from here.

PHIRE - this Visual Basic program performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge. ( Reference: Lavigne, R. et al. 2004. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatika 20: 629-635).

MB DNA Analysis (Oleg Simakov) - MB is a free multi-functional DNA/protein analysis program. It's main advantage is that it combines all of the most widely used features needed for an advanced molecular analysis of genomic/proteomic data. Features of MB include a fast restriction analysis algorithm (included plasmid / linear DNA drawing), promoter analysis, calculation of molecular weights and chemical properties of proteins, prediction of the secondary protein structures (after Chou-Fasman). Protein analysis also includes sequence translation and codon usage table calculation. Other features: hierarchical multiple sequence alignment tool (with a feature to compare secondary structure of proteins), phylogenetic tree building, dot plot, estimation of isoelectric point for proteins, primer design. A tool for the structural analysis of alpha helices is also included in the main package.
GenePalette allows genome sequence visualization and navigation. Users can download from NCBI&rsquos GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.

UGene (UniPro Bioinformatics Group, Russia) - without a doubt one of the best software packages for genome annotation ( Reference: Okonechnikov K et al. 2012. Bioinformatics 28: 1166-1167).

Artemis: a DNA sequence viewer and annotation tool (Sanger Centre)

SEQtools is a program package for routine handling and analysis of DNA and protein sequences. The package includes general facilities for sequence and contig editing, restriction enzyme mapping, translation, and repeat identification. Free for students

DNA Club - DNA analysis software, features include remove vector sequence, find, find ORF, sequence editing, translate to protein sequence, protein sequence editing, RE Map, RE Map with translation, PCR primer selection, primer or probe evaluation etc.

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.

RNAdraw - is an integrated program for RNA secondary structure calculation and analysis by Ole Matzura & Anders Wennborg (1996) Computer Applications in the Biosciences (CABIOS) 12: 247-249

RNAstructure - RNA Secondary Structure Prediction and Analysis for Microsoft Windows. This program includes a secondary structure prediction algorithm, a sequence editor, an integrated drawing tool, the OligoWalk program, OligoScreen, Dynalign, and a partition function calculator. (Verwysing: 21: 2246 - 2253.)

Chromas will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create. N.B. only the older versions of the software are free.

FinchTV - Another useful tool for viewing and editing electropherograms.

G-language Genome Analysis Environment provides a greater variety of useful genome analysis tools compared to most existing analysis software packages, and is also easily pluggable. All of its tools are accessible as Perl modules. To get started download genome files from GenBank in *.gbk format (GenBank flat file format).


DNA Master - is "perhaps the world's greatest sequence editor" and analysis package. Find under "computer."

GeSTer (V. Nagaraja, I ndian Institute of Science, Bangalore. India ) - is extremely useful in locating stem-loop structures, including rho-independent terminators in annotated genomes. Since it does not run conveniently on Windows XP see how you can modify the *.gbk file so that it works.

Staden Package - consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin). The package was originally developed at the MRC-LMB in Cambridge. It is now open source (BSD licence) and is hosted on sourceforge.net.

Seqool - sequence analysis software designed primarily for searching biological signals in nucleic acid sequences. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc.

GENtle - software package for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

RepeatAround - is designed to find &ldquodirect repeats&rdquo, &ldquoinverted repeats&rdquo, &ldquomirror repeats&rdquo and &ldquocomplementary repeats&rdquo, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database or simple sequence. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats. ( Reference: Goios A et al. 2006. Mitochondrion 6: 218-224) .

ACUA (Automated Codon Usage Analysis Bioinsilico Technologies ) - is a Visual Basic based interface for the Insilico codon analysis. This tool provides various unique features like, Nucleotide analysis, statistical codon analysis. The tool performs Nucleotide analysis for the query sequence(s), and presents the results in spreadsheets, which can be further utilized for statistical analysis. This tool will prove to be highly useful for the scientists who would like to do codon analysis for multiple sequence simultaneously.

SnapGene Viewer - includes the same rich visualization, annotation, and sharing capabilities as the fully enabled SnapGene software. I am very impressed with this freeware which enabled me to produce this map from the gbk file.

pLOT (Jean-Marc DeKeyser, Vanderbilt University, U.S.A.)

ApE Plasmid Editor (M. Wayne Davis, Univ. Utah, U.S.A.) highlights and draws graphic maps using feature annotations from GenBank and EMBL files creates graphic restriction maps - linear or circular with features indicated and allows BLAST analyses along with a number of other useful features.

pDRAW32 DNA analysis software by AcaClone software (Kjeld Olesen). pDRAW lets you enter a DNA name and coordinates for genetic elements, such as genes, to be plotted on your DNA plots.

BVTech Plasmid - with this program you can draw circular or linear plasmid map with double strands or single strand. You can label the plasmid with genes and restriction sites in different colors, text, and styles.

Plasmid Drawing Program: Plasmidomics 0.2 (Robert Winkler, Cinvestav Unidad Irapuato, Mexico)

Picky is an oligo microarray design program that identifies probes that are very unique and specific to input sequences. These calculations are based on parameters inputted by the user including optimal probe length, ideal percentage of guanine and cytosine content, target-melting temperature, salt concentration and the maximum length to which a target sequence matches any non-target sequence. ( Reference: H.-H. Chou et al. (2004) Bioinformatics 20: 2893-2902).Download genome *.ffn files from GenBank for use with this program. N.B. Unfortunately these files do not include the gene names only their coordinates.

AiO (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning. AiO uses databases that allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment. ( Reference: Karreman C. (2002) Bioinformatics. 18:884-885).

- Oligo Analyzer is a simple tool to determine primer properties like Tm, GC%, primer loops, primer dimers and primer-primer compatibility. All you have to do is to paste or type primer sequence and let Oligo Analyzer to calculate all important primer properties mentioned above. Readme

- Oligo Explorer is a tool to search primers and primer pairs. The program analyzes all important primer properties like Tm, GC%, primer loops, primer dimers and etc. Readme

AnnHyb This programs features include sequence editing with proofreading, format conversion, translation, sequence statistics, probe design & analysis.

- MeltCalc is the ultimate thermodynamic modelling spreadsheet for Excel&trade which allows you to analyze probes. See: Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches ( Reference: Schütz, E., von Ahsen, N. (1999) BioTechniques 27:1218-1224).

ANTHEPROT (ANalyse THE PROTeins) is the result of biocomputing activity at the Institute of Biology and Chemistry of Proteins (Lyon, France)

STORM - this program extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties. The raw output for these analyses is then analysed and summarized. ( Reference: Lavigne, R. et al. (2003.) Applied Bioinformatics 2: 177-179).

VESPA (Visual Evaluation and Statistics to Promote Annotation) targeted at the integration of peptide-centric proteomics data with other forms of high-throughput, qualitative and quantitative data, such as data from Ref-SEQ analyses. At the core, VESPA integrates bottom-up proteomics data with genome level information, i.e., mapping peptides to their respective genome locations. This capability is a necessity in proteogenomics where scientists are correcting either mis-annotations or identifying new genes. The visualization allows the user to observe the location and sequence of peptides that do not match current annotations, as well as offering valuable filtering criteria such as the removal of ambiguous peptides.

Yasara (Gregor Högenauer, Günther Koraimann, & Andreas Kungl [Univ. Graz, Austria] & Gert Vriend [Univ. Nijmegen, the Netherlands]) is an awesome program for viewing an labeling 3-D structures. To visual your own pdb structure right click and chose open with (Yasara). This free program is part of a more extensive molecular modeling package.

RasMol is software for looking at molecular structures. It is very fast: rotating a protein or DNA molecule shows its 3D structure.

Deep View (Swiss-PdbViewer) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface

- Biodesigner is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models.

RasTop - RasTop is a molecular visualization software adapted from the program RasMol by wrapping a user-friendly graphical interface around the "RasMol molecular engine". The software allows several molecules to be opened in the same window and several windows to be opened at the same time. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

ClustalX is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. ( Reference: J.D. Thompson et al. (1997). Nucleic Acids Research 24: 4876-4882).

VennPlex - a program that illustrates the often diverse numerical interactions among multiple, high-complexity datasets, using up to four data sets. VennPlex includes versatile output features, where grouped data points in specific regions can be easily exported into a spreadsheet. This program is able to facilitate the analysis of two to four gene sets and their corresponding expression values in a user-friendly manner. ( Reference: Cai H et al. (2013) PLoS One 8(1): e53388).

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by Tom Hall (North Carolina State University). It also provides BLAST capability on local databases.

CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic). The formatted annotation can be sent directly into Microsoft Word, or saved to a file or Windows Clipboard in both HTML and "Rich Text" Formats. ( Reference: L. Goodstadt & C.P. Ponting. (2001) Bioinformatics 17: 845-846).

SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows ones to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally improve the alignment.

Sequence Demarcation Tool (SDTv1.2) is a free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results. The identity scores are calculated as 1-(M/N) where M is the number of mismatching nucleotides and N the total number of positions along the alignment at which neither sequence has a gap character. ( Reference: Muhire BM et al. (2014) PLoS ONE 9(9): e108277).

HyPhy - intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more ( Reference: S.L. Kosakovsky et al.(2005) Bioinformatics 21:676-679).

ChromaClade - is a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. ( Reference: Monit C et al. (2019) BMC Evol Biol 19: 186).

TREECON - is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. It offers considerable opportunity to change the appearance of the tree. ( Reference: Van de Peer, Y. & De Wachter, Y. (1994) Comput. Applic. Biosci. 10, 569-570).

Treefinder (Gangolf Jobb, Statistical Genetics and Bioinformatics, University of Munich) computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method, it is offering a variety of evolutionary models up to the general time reversible model with Gamma and codon position rate heterogeneity among sites. The confidence of inferred relationships may be assessed by bootstrap analysis or, alternatively, by a local rearrangement paired-sites method (LRP). Linus and Mac versions also available.

MEGA - an incredible phylogenetic analysis program. ( Reference: S. Kumar et al. (2001) Bioinformatics 17: 1244-1245)..

Tree-Puzzle (H.A. Schmidt, K. Strimmer, M. Vingron, & A. von Haeseler, Germany) constructs phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock- assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies. PHYLIP is the most widely-distributed phylogeny package, and competes with PAUP to be the one responsible for the largest number of published trees (Joe Felsenstein, University of Washington, U.S.A.).

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints.

PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.

NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. Written by Manolo Gouy.

Orthologous Average Nucleotide Identity Tool (OAT) - OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95

96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. ( Reference: Lee, I. et al. (2015). Int J Syst Evol Microbiol. 66: 1100-1103).

SeqVerter is a sequence file format conversion utility by GeneStudio, Inc.

DynaFit - Perform nonlinear least-squares regression on chemical or enzymatic kinetic data.

PrestoPlot - 2D plotting tool

Xenu's Link Sleuth (TM) is a spidering software that checks Web sites for broken links. Link verification is done on "normal" links, images, frames, plug-ins, backgrounds, local image maps, style sheets, scripts and java applets. It displays a continously updated list of URLs which you can sort by different criteria. I use this program to verify if the links on Online Analysis Tools are working.

Paint.NET is a photo and image editing tool designed for computers running Microsoft Windows XP or Windows 2000. It serves the digital imaging community as a free alternative to the standard paint application included with Windows. It brings powerful features to the desktop, a myriad of special effects, plug-in extensibility, and layer manipulation. It enhances the image editing experience for tablet owners with Windows XP Tablet Ink support. Digital photographers and artists can enhance their images with features and effects such as levels adjustment, cross-layer cloning, anti-aliased tools, motion blur, and red eye removal.

TinyQuant is a graphical display program designed for analysis and limited manipulation of images obtained by scanning of gels or autoradiographs. Useful for integrating densities of gel bands in 16 bit greyscale (PC or Mac format ".gel" or TIFF files) or 24 bit RGB TIFF images, and for converting these to 8 bit greyscale TIFFs.

A Smaller GIF - Pedagoguery Software Inc. provides a variety of free software packages for both Macintosh and Windows computers. This program reduces the size of animated GIFs without affecting their appearance in any way.

UTHSCSA ImageTool (Dental Diagnostic Science, University of Texas Health Science Center, San Antonio, U.S.A.) - can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. IT can read and write over 22 common file formats including BMP, PCX, TIF, GIF and JPEG. Image analysis functions include dimensional (distance, angle, perimeter, area) and gray scale measurements (point, line and area histogram with statistics). ImageTool supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection, median filtering and spatial convolutions with user-defined convolution masks.

GIMP is the GNU Image Manipulation Program. It is a freely distributed piece of software for such tasks as photo retouching, image composition and image authoring. It works on many operating systems, in many languages. The GIMP animation package, is also now available

ACD/ChemSketch (Advanced Chemistry Development, Inc) - for drawing chemical structures and graphical images.


Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ PUBMED:11297922 , PUBMED:11290319 ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ PUBMED:11290319 , PUBMED:11114498 ].

This ribosomal protein is found in archaebacteria and eukaryotes [ PUBMED:2546769 ]. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [ PUBMED:8484768 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.


HMM information

Sunburst controls

Weight segments by.

Change the size of the sunburst

Colour assignments

Archea Eukaryota
Bakterieë Other sequences
Virusse Unclassified
Viroïede Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Currently selected:

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab . Meer.

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.


Verwysings

  1. ^ ab El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer EL, Hirsh L, Paladin L, Piovesan D, Tosatto SC, Finn RD (January 2019). "The Pfam protein families database in 2019". Nukleïensure Navorsing. 47 (D1): D427–D432. doi:10.1093/nar/gky995. PMC  6324024 . PMID�.
  2. ^ ab Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC  2954198 . PMID�.
  3. ^ Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (January 2012). "The Pfam protein families database". Nukleïensure Navorsing. 40 (Database issue): D290–301. doi:10.1093/nar/gkr1065. PMC  3245129 . PMID�.
  4. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Verrigtinge van die National Academy of Sciences van die Verenigde State van Amerika. 95 (11): 5857–64. Bibcode:1998PNAS. 95.5857S. doi:10.1073/pnas.95.11.5857. PMC  34487 . PMID�.
  5. ^ Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A (September 2009). "Exploration of uncharted regions of the protein universe". PLoS Biology. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC  2744874 . PMID�.
  6. ^ Mudgal R, Sandhya S, Chandra N, Srinivasan N (July 2015). "De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods". Biology Direct. 10 (1): 38. doi:10.1186/s13062-015-0069-2. PMC  4520260 . PMID�.
  7. ^ abc Goodacre NF, Gerloff DL, Uetz P (December 2013). "Protein domains of unknown function are essential in bacteria". mBio. 5 (1): e00744–13. doi:10.1128/mBio.00744-13. PMC  3884060 . PMID�.
  8. ^ abc Häuser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P (2012). Hughes D (ed.). "RsfA (YbeB) proteins are conserved ribosomal silencing factors". PLoS Genetics. 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC  3400551 . PMID�.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.


Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green . Let op that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Let op that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted .

You can use the tree controls to manipulate how the interactive tree is displayed:

  • show/hide the summary boxes
  • highlight species that are represented in the seed alignment
  • expand/collapse the tree or expand it to a given depth
  • select a sub-tree or a set of species within the tree and view them graphically or as an alignment
  • save a plain text representation of the tree

Neem asseblief kennis: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


Kyk die video: Using UNIPROT u0026 GenBank to Locate Gene Sequences Given a Known Protein (Oktober 2022).