411 lines
17 KiB
R
411 lines
17 KiB
R
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# create_refDB.R
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# Create a reference protein database for Mbp1-like proteins
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#
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# Boris Steipe for BCH441
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#
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# For the species, see:
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# cf. http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi
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#
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# For the schema, see dbInit() in .utilities.R
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#
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# ==============================================================================
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refDB <- dbInit()
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# === protein table ===
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_ASPNI",
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RefSeqID = "XP_660758",
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UniProtID = "Q5B8H6",
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taxonomy.ID = as.integer(162425),
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sequence = dbSanitizeSequence("
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MAAVDFSNVYSATYSSVPVYEFKIGTDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGT
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WIPLQEGRQLAERNNILDKLLPIFDYVAGDRSPPPAPKHTSAASKPRAPKINKRVVKEDVFSAVNHHRSMGPPSFHHEHY
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DVNTGLDEDESIEQATLESSSMIADEDMISMSQNGPYSSRKRKRGINEVAAMSLSEQEHILYGDQLLDYFMTVGDAPEAT
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RIPPPQPPANFQVDRPIDDSGNTALHWACAMGDLEIVKDLLRRGADMKALSIHEETPLVRAVLFTNNYEKRTFPALLDLL
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LDTISFRDWFGATLFHHIAQTTKSKGKWKSSRYYCEVALEKLRTTFSPEEVDLLLSCQDSVGDTAVLVAARNGVFRLVDL
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LLSRCPRAGDLVNKRGETASSIMQRAHLAERDIPPPPSSITMGNDHIDGEVGAPTSLEPQSVTLHHESSPATAQLLSQIG
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AIMAEASRKLTSSYGAAKPSQKDSDDVANPEALYEQLEQDRQKIRRQYDALAAKEAAEESSDAQLGRYEQMRDNYESLLE
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QIQRARLKERLASTPVPTQTAVIGSSSPEQDRLLTTFQLSRALCSEQKIRRAAVKELAQQRADAGVSTKFDVHRKLVALA
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TGLKEEELDPMAAELAETLEFDRMNGKGVGPESPEADHKDSASLPFPGPVVSVDA"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_BIPOR",
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RefSeqID = "XP_007682304",
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UniProtID = "W6ZM86",
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taxonomy.ID = as.integer(101162),
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sequence = dbSanitizeSequence("
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MPPAPDGKIYSATYSNVPVYECNVNGHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKVQGGYGKYQGT
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WIPLEEGRGLAERNGVLDKMRAIFDYVPGDRSPPPAPKHATAASNRMKPPRQTAAAVAAAAVAAAAAAAAVANHNALMSN
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SRSQASEDPYENSQRSQIYREDTPDNETVISESMLGDADLMDMSQYSADGNRKRKRGMDQMSLLDQQHQIWADQLLDYFM
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LLDHEAAVSWPEPPPSINLDRPIDEKGHAAMHWAAAMGDVGVVKELIHRGARLDCLSNNLETPLMRAVMFTNNFDKETMP
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SMVKIFQQTVHRTDWFGSTVFHHIAATTSSSNKYVCARWYLDCIINKLSETWIPEEVTRLLNAADQNGDTAIMIAARNGA
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RKCVRSLLGRNVAVDIPNKKGETADDLIRELNQRRRMHGRTRQASSSPFAPAPEHRLNGHVPHFDGGPLMSVPVPSMAVR
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ESVQYRSQTASHLMTKVAPTLLEKCEELATAYEAELQEKEAEFFDAERVVKRRQAELEAVRKQVAELQSMSKGLHIDLND
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EEAERQQEDELRLLVEEAESLLEIEQKAELRRLCSSMPQQNSDSSPVDITEKMRLALLLHRAQLERRELVREVVGNLSVA
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GMSEKQGTYKKLIAKALGEREEDVESMLPEILQELEEAETQERAEGLDGSPV"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_NEUCR",
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RefSeqID = "XP_955821",
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UniProtID = "Q7RW59",
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taxonomy.ID = as.integer(5141),
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sequence = dbSanitizeSequence("
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MVKENVGGNPEPGIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREVQKDTHEKIQG
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GYGRYQGTWIPLEQAEALARRNNIYERLKPIFEFQPGNESPPPAPRHASKPKAPKVKPAVPTWGSKSAKNANPPQPGTFL
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PPGRKGLPAQAPDYNDADTHMHDDDTPDNLTVASASYMAEDDRYDHSHFSTGHRKRKRDELIEDMTEQQHAVYGDELLDY
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FLLSRNEQPAVRPDPPPNFKPDWPIDNERHTCLHWASAMGDVDVMRQLKKFGASLDAQNVRGETPFMRAVNFTNCFEKQT
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FPQVMKELFSTIDCRDLSGCTVIHHAAVMKIGRVNSQSCSRYYLDIILNRLQETHHPEFVQQLLDAQDNDGNTAVHLAAM
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RDARKCIRALLGRGASTDIPNKQGIRAEELIKELNASISKSRSNLPQRSSSPFAPDTQRHDAFHEAISESMVTSRKNSQP
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NYSSDAANTVQNRITPLVLQKLKDLTATYDSEFKEKDDAEKEARRILNKTQSELKALTASIDDYNSRLDTDDVAAKTAAE
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MATARHKVLAFVTHQNRISVQEAVKQELAALDRANAVTNGTSTKSKSSSPSKKPKLSPIPDQKDKPPKDENETESEAEHP
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DPPAAQAHQQQPGPSSQDTEVEDQDREEEEDDYTHRLSLAAELRSILQEQRSAENDYVEARGMLGTGERIDKYKHLLMSC
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LPPDEQENLEENLEEMIKLMEQEDESVTDLPAGAVGGGGGGNAADGSGGGGQPSNGRRESVLPALRGGNGDGEMSRRGSR
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TAAAAAAQVDGEREINGRAGAERTERIQEIAAV"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_SACCE",
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RefSeqID = "NP_010227",
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UniProtID = "P39678",
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taxonomy.ID = as.integer(4932),
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sequence = dbSanitizeSequence("
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MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
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GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET
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KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL
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PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ
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QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV
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NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS
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IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL
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SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM
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MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ
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MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK
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KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS
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LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_SCHPO", # actually the Res2 protein
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RefSeqID = "NP_593032",
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UniProtID = "P41412",
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taxonomy.ID = as.integer(4896),
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sequence = dbSanitizeSequence("
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MAPRSSAVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTW
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VPFQRGVDLATKYKVDGIMSPILSLDIDEGKAIAPKKKQTKQKKPSVRGRRGRKPSSLSSSTLHSVNEKQPNSSISPTIE
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SSMNKVNLPGAEEQVSATPLPASPNALLSPNDNTIKPVEELGMLEAPLDKYEESLLDFFLHPEEGRIPSFLYSPPPDFQV
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NSVIDDDGHTSLHWACSMGHIEMIKLLLRANADIGVCNRLSQTPLMRSVIFTNNYDCQTFGQVLELLQSTIYAVDTNGQS
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IFHHIVQSTSTPSKVAAAKYYLDCILEKLISIQPFENVVRLVNLQDSNGDTSLLIAARNGAMDCVNSLLSYNANPSIPNR
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QRRTASEYLLEADKKPHSLLQSNSNASHSAFSFSGISPAIISPSCSSHAFVKAIPSISSKFSQLAEEYESQLREKEEDLI
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RANRLKQDTLNEISRTYQELTFLQKNNPTYSQSMENLIREAQETYQQLSKRLLIWLEARQIFDLERSLKPHTSLSISFPS
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DFLKKEDGLSLNNDFKKPACNNVTNSDEYEQLINKLTSLQASRKKDTLYIRKLYEELGIDDTVNSYRRLIAMSCGINPED
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LSLEILDAVEEALTREK"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_COPCI",
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RefSeqID = "XP_001837394",
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UniProtID = "A8NYC6",
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taxonomy.ID = as.integer(5346),
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sequence = dbSanitizeSequence("
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MPEAQIFKATYSGIPVYEMMCKGVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIP
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LERGMQLAKQYNCEHLLRPIIEFTPAAKSPPLAPKHLVATAGNRPVRKPLTTDLSAAVINTRSTRKQVADGVGEESDHDT
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HSLRGSEDGSMTPSPSEASSSSRTPSPIHSPGTYHSNGLDGPSSGGRNRYRQSNDRYDEDDDASRHNGMGDPRSYGDQIL
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EYFISDTNQIPPILITPPPDFDPNMAIDDDGHTSLHWACAMGRIRIVKLLLSAGADIFKVNKAGQTALMRSVMFANNYDV
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RKFPELYELLHRSTLNIDNSNRTVFHHVVDVAMSKGKTHAARYYMETILTRLADYPKELADVINFQDEDGETALTMAARC
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RSKRLVKLLIDHGADPKINNHDGKNAEDYILEDERFRSSPAPSSRVAAMSYRNAQVAYPPPGAPSTYSFAPANHDRPPLH
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YSAAAQKASTRCVNDMASMLDSLAASFDQELRDKERDMAQAQALLTNIQAEILESQRTVLQLRQQAEGLSQAKQRLADLE
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NALQDKMGRRYRLGFEKWIKDEETREKVIRDAANGDLVLTPATTSYTVDEDGDSDSGSNGDKNKGKRKAQVQQEEVSDLV
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ELYSNIPTDPEELRKQCEALREEVSQSRKRRKAMFDELVTFQAEAGTSGRMSDYRRLIAAGCGGLEPLEIDSVLGMLLET
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LEAEDPSSTSATWSGSKGQQTG"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_CRYNE",
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RefSeqID = "XP_569090",
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UniProtID = "Q5KMQ9",
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taxonomy.ID = as.integer(5207),
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sequence = dbSanitizeSequence("
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MGKKVIASGGDNGPNTIYKATYSGVPVYEMVCRDVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQG
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GYGKYQGTWIPIERGLALAKQYGVEDILRPIIDYVPTSVSPPPAPKHSVAPPSKARRDKEKETGRTKATPSRTGPTSAAA
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LQAQAQLNRAKMHDSTPDADASFRSFEERVSLTPEDDSSSDTPSPVASVMTDQDMEVDKMGMHMSMPNVTLSQNMEELGA
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GSRKRSAAMMMEDEDQFGQLRSIRGNSAVHTPHGTPRHLGIGMPPEPIGPEQYTDIILNYFVSETSQIPSILVSPPHDFD
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PNAPIDDDGHTALHWACAMGRVRVVKLLLTAGASIFAGNNAEQTPLMRSVMFSNNYDMRKFPELYELLHRSTLNIDKQNR
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TVFHHIANLALTKGKTHAAKYYMETILARLADYPQELADVINFQDEEGETALTIAARARSRRLVKALLDHGANPKIKNRD
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SRSAEDYILEDERFRSSPVPAPNGGIGKASTSAAAEKPLFAPQLYFSEAARLCGGQALTDITSHMQSLARSFDAELQGKE
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RDILQAKALLTNIHTEVTENGRSITAITNQAAPLEEKRRELEALQASLKTRVKDALKKGYIGWLEGELVREQRWENGELE
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GNEEEKAAVQALRDVPTGGQEVVQAEEEKLRWEIEEKRKRRAMFVEKFVRAQTEAGTSEQIAKYRKLVSAGLGGVSTNEV
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DELMNQLLEGLEEENDNQVYNTTAGESGPSSWVQ"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_PUCGR",
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RefSeqID = "XP_003327086",
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UniProtID = "E3KED4",
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taxonomy.ID = as.integer(5297),
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sequence = dbSanitizeSequence("
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MAYGGSIQPLRPPSRESATLHLHQPDLTVTSPPLSLTHCPPCVYSHFTHTPTSLIVIQVSLHSLLDQETYHLLPSRSPPT
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VSVRMGTTTIYKATYSGVPVLEMPCEGIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREIQKGTHEKIQGGYGKYQG
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TWVPLDRGIDLAKQYGVDHLLSALFNFQPSSNESPPLAPKHVTALSTRVKVSKVSAASAARAARAVVPSLPSTSGLGGRN
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TNNSWSNFDSDNEPGLPPAASSRESNGNWATQSKLARSSNLARARANINNSHPEDLPVPAPDQLQASPLPSMQTADPEND
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NSLTPSELSLPSRTPSPIEDLPLTVNTASSQSTRNKGKSRDLPDDEDLSRGQKRKYDTSLVEDTSYSDGADDQYINGNPS
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NAASAKYAKLILDYFVSESSQIPNFLNDPPSDFDPNVVIDDDGHTALHWACAMGRIKIIKLLLTCGADIFRANNAGQTAL
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MRAVMFTNNHDLRTFPELFESFSGSVINIDRTDRTVFHYVIDIALTKGKVPAARYYLETILSQLSEYPKELIDILNFQDE
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DGETALTLAARCRSKKLVKILLDHGANPKTANRDGKSAEDYILEDDKFRALSPTPCSSGPIRQLDQNSPGGTSNRSDFVD
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LVDPVPIDSNLIPQRSPNASPPHYSETGQRVTKQLLPEVTSMIELLATTFDTELQDKERDLDHAVGLLSNIEKEYLEGQR
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KILNYERMLSDFGEKKLALGDLEKELNDKLGKRYRFGWEKYVRDEEERARRITEQRSKYLQELSIEDRKLLDSSNLRFAD
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PSKQEVLMKLQADERENSDLLNLIRTNSTDVESECDLLRESVQKLSEERERLFKEFINLSSENTGGENEEDDGANHTSAN
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TSRLNNYRKLISLGCGGIGLDEVDEVIESLNEGIDVNELNDNGFLTEQDEELGNHQNYHNIHTQGR"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_USTMA",
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RefSeqID = "XP_011392621",
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UniProtID = "A0A0D1DP35",
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taxonomy.ID = as.integer(5270),
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sequence = dbSanitizeSequence("
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MSGDKTIFKATYSGVPVYECIINNVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWI
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PLDVAIELAERYNIQGLLQPITSYVPSAADSPPPAPKHTISTSNRSKKIIPADPGALGRSRRATSIETESEVIGAAPNNV
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SEGSMSPSPSDISSSSRTPSPLPADRAHPLHANHALAGYNGRDANNHARYADIILDYFVTENTTVPSLLINPPPDFNPDM
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SIDDDEHTALHWACAMGRIRVVKLLLSAGADIFRVNSNQQTALMRATMFSNNYDLRKFPELFELLHRSILNIDRNDRTVF
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HHVVDLALSRGKPHAARYYMETMINRLADYGDQLADILNFQDDEGETPLTMAARARSKRLVRLLLEHGADPKIRNKEGKN
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AEDYIIEDERFRSSPSRTGPAGIELGADGLPVLPTSSLHTSEAGQRTAGRAVTLMSNLLHSLADSYDSEINTAEKKLTQA
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HGLLKQIQTEIEDSAKVAEALHHEAQGVDEERKRVDSLQLALKHAINKRARDDLERRWSEGKQAIKRARLQAGLEPGALS
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TSNATNAPATGDQKSKDDAKSLIEALPAGTNVKTAIAELRKQLSQVQANKTELVDKFVARAREQGTGRTMAAYRRLIAAG
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CGGIAPDEVDAVVGVLCELLQESHTGARAGAGGERDDRARDVAMMLKGAGAAALAANAGAP"),
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stringsAsFactors = FALSE))
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refDB$protein <-
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rbind(refDB$protein,
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data.frame(
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ID = dbAutoincrement(refDB$protein$ID, ns = "ref"),
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name = "MBP1_WALME",
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RefSeqID = "XP_006957051",
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UniProtID = "I4YGC0",
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taxonomy.ID = as.integer(1708541),
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sequence = dbSanitizeSequence("
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MSAPPIYKACYSGVPVYEFNCKNVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGGYGKYQGTWIP
|
||
|
|
MERSVELARQYRIELLLDPIINYLPGPQSPPLAPKHATNVGSRARKSTAPAAQTLPSTSKVFHPLSSTKHPAKLAAATNA
|
||
|
|
KAEISDGEDASIPSSPSFKSNSSRTPSPIRINARKRKLEDEATIPSSAIDGSISYEDIILDYFISESTQIPALLIHPPSD
|
||
|
|
FNPNMSIDDEGHTAMHWACAMGKVRVVKLLLSAGADIFRVNHSEQTALMRSVMFSNNYDIRKFPQLYELLHRSTLNLDKH
|
||
|
|
DRTVLHHIVDLALTKSKTHAARYYMECVLSKLANYPDELADVINFQDDEGESALTLAARARSKRLVKLLLEHGADSKLPN
|
||
|
|
KDGKTAEDYILEDERFRQSPLLNSNHLRLHPPDTSIYAPPAHLFNSETSQNIANTSMSSVANLLESLAQSYDKEITQKER
|
||
|
|
DYQQAQVILRNIKTDIVEAKSNIEKMTIDSSEFEHLKHKLRELEMKLEEHSNDVYNKGWEEYSRNVDDPAIDAPSDNVQE
|
||
|
|
ECASLRNKIKDLQEKRISSMQELIKRQKEVGTGKKMSEYRKLISVGCGIPTTEIDAVLEMLLESLESENANKKAALASGI
|
||
|
|
SGALSSTSSAPSQATTSAPTGVATPGAPVPASSEKAGLLPPAPVMQ"),
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
# === taxonomy table ===
|
||
|
|
|
||
|
|
refDB$taxonomy <-
|
||
|
|
rbind(refDB$taxonomy,
|
||
|
|
data.frame(
|
||
|
|
ID = as.integer(c(162425,
|
||
|
|
101162,
|
||
|
|
5141,
|
||
|
|
4932,
|
||
|
|
4896,
|
||
|
|
5346,
|
||
|
|
5207,
|
||
|
|
5297,
|
||
|
|
5270,
|
||
|
|
1708541)),
|
||
|
|
species = c("Aspergillus nidulans",
|
||
|
|
"Bipolaris oryzae",
|
||
|
|
"Neurospora crassa",
|
||
|
|
"Saccharomyces cerevisiae",
|
||
|
|
"Schizosaccharomyces pombe",
|
||
|
|
"Coprinopsis cinerea",
|
||
|
|
"Cryptococcus neoformans",
|
||
|
|
"Puccinia Graminis",
|
||
|
|
"Ustilago maydis",
|
||
|
|
"Wallemia mellicola"),
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === feature table ===
|
||
|
|
|
||
|
|
refDB$feature <-
|
||
|
|
rbind(refDB$feature,
|
||
|
|
data.frame(
|
||
|
|
ID = c("ref_ftr_1",
|
||
|
|
"ref_ftr_2",
|
||
|
|
"ref_ftr_3",
|
||
|
|
"ref_ftr_4",
|
||
|
|
"ref_ftr_5",
|
||
|
|
"ref_ftr_6",
|
||
|
|
"ref_ftr_7",
|
||
|
|
"ref_ftr_8"),
|
||
|
|
name = c("APSES fold",
|
||
|
|
"KilA-N",
|
||
|
|
"AT hook",
|
||
|
|
"low complexity",
|
||
|
|
"Ankyrin",
|
||
|
|
"Swi6 fold",
|
||
|
|
"coiled coil",
|
||
|
|
"McInerny 2011"),
|
||
|
|
type.ID = rep("ref_typ_1", 8),
|
||
|
|
description = c("DNA binding domain by similarity to structure",
|
||
|
|
"DNA binding domain by Pfam annotation",
|
||
|
|
"DNA interaction motif by SMART annotation",
|
||
|
|
"SEG annotation by SMART",
|
||
|
|
"Ankyrin domain by SMART annotation",
|
||
|
|
"Swi6 fold by similarity to structure",
|
||
|
|
"Coiled coil by SMART annotation",
|
||
|
|
"Yeast cell cycle review"),
|
||
|
|
sourceDB = c("PDB",
|
||
|
|
"Pfam",
|
||
|
|
"SMART",
|
||
|
|
"SMART",
|
||
|
|
"SMART",
|
||
|
|
"PDB",
|
||
|
|
"SMART",
|
||
|
|
"PubMed"),
|
||
|
|
accession = c("1BM8_A_1_99",
|
||
|
|
"PF04383",
|
||
|
|
NA,
|
||
|
|
NA,
|
||
|
|
"SM00248",
|
||
|
|
"1SW6_B",
|
||
|
|
NA,
|
||
|
|
NA),
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
# === protein annotation table ===
|
||
|
|
|
||
|
|
# there are many! This, we don't code explicitly, but read from a textfile
|
||
|
|
# I have prepared.
|
||
|
|
|
||
|
|
tmp <- read.table("referenceDomainAnnotations.txt",
|
||
|
|
header = TRUE,
|
||
|
|
sep = "\t",
|
||
|
|
comment.char = "#",
|
||
|
|
strip.white = TRUE,
|
||
|
|
stringsAsFactors = FALSE)
|
||
|
|
|
||
|
|
# remove the notes column - that is in the text file, only for our reference,
|
||
|
|
# not part of the data model
|
||
|
|
tmp <- tmp[ , -(ncol(tmp))]
|
||
|
|
|
||
|
|
# add table IDs
|
||
|
|
for (i in 1:nrow(tmp)) {
|
||
|
|
tmp[i, "ID"] <- dbAutoincrement(tmp$ID, ns = "ref", code = "fan")
|
||
|
|
}
|
||
|
|
|
||
|
|
# add table to DB
|
||
|
|
refDB$proteinAnnotation <-
|
||
|
|
rbind(refDB$proteinAnnotation,
|
||
|
|
tmp)
|
||
|
|
|
||
|
|
|
||
|
|
# === system table ===
|
||
|
|
|
||
|
|
refDB$system <-
|
||
|
|
rbind(refDB$system,
|
||
|
|
data.frame(
|
||
|
|
ID = "ref_sys_1",
|
||
|
|
name = "G1/S SACCE",
|
||
|
|
notes = paste("Regulates transition from G1 to S phase",
|
||
|
|
"in the yeast cell cycle."),
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === component table ===
|
||
|
|
|
||
|
|
refDB$component <-
|
||
|
|
rbind(refDB$component,
|
||
|
|
data.frame(
|
||
|
|
ID = "ref_cmp_1",
|
||
|
|
protein.ID = "ref_pro_4", # MBP1_SACCE
|
||
|
|
system.ID = "ref_sys_1", # G1/S SACCE
|
||
|
|
status = "include",
|
||
|
|
notes = paste("Part of MBF complex."),
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === system annotation table ===
|
||
|
|
|
||
|
|
refDB$systemAnnotation <-
|
||
|
|
rbind(refDB$systemAnnotation,
|
||
|
|
data.frame(
|
||
|
|
ID = "ref_san_1",
|
||
|
|
system.ID = "ref_sys_1", # G1/S SACCE
|
||
|
|
feature.ID = "ref_ftr_8", # PubMed
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === component annotation table ===
|
||
|
|
|
||
|
|
refDB$componentAnnotation <-
|
||
|
|
rbind(refDB$componentAnnotation,
|
||
|
|
data.frame(
|
||
|
|
ID = "ref_can_1",
|
||
|
|
component.ID = "ref_cmp_1", # Mbp1 in G1/S SACCE
|
||
|
|
feature.ID = "ref_ftr_8", # PubMed
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === type table ===
|
||
|
|
|
||
|
|
refDB$type <-
|
||
|
|
rbind(refDB$type,
|
||
|
|
data.frame(
|
||
|
|
ID = "ref_typ_0",
|
||
|
|
name = "UNDEF",
|
||
|
|
description = "Undefined type",
|
||
|
|
stringsAsFactors = FALSE))
|
||
|
|
|
||
|
|
|
||
|
|
# === save
|
||
|
|
|
||
|
|
save(refDB, file = "data/refDB.RData")
|
||
|
|
|
||
|
|
# [END]
|