#!/usr/bin/perl # PROGRAM : simplealign.pl # PURPOSE : Simple driver for Bio::SimpleAlign # AUTHOR : Ewan Birney birney@sanger.ac.uk # CREATED : Tue Oct 27 1998 # # INSTALLATION # If you have installed bioperl using the standard # makefile system everything should be fine and # dandy. # # if not edit the use lib "...." line to point the directory # containing your Bioperl modules. # #use lib "/nfs/disk21/birney/prog/bioperl/"; # Modified 3/5/01 to use AlignIO by Peter Schattner schattner@alum.mit.edu # # This uses the internal DATA stream (past the end of this # file, on the __END__ tag) to load in the data. We then # do some reformats, sort in a different way and a quick # getting into the alignment. All pretty simple ;) # # # The simplealign module does not do the following things # a) give you sensible ways of asking if residues are a # column of gaps or conservation # b) provide ways of editing the alignment # c) making alignments # # # a) and b) are probably best done by UnivAlign from Georg Fuellen # c) is done for pairwise alignments in Bio::Tools::pSW; and # also you can read in stuff from programs like clustal and hmmer # into this. # use strict; use Bio::SimpleAlign; use Bio::AlignIO; # read from a stream my $str = Bio::AlignIO->newFh('-fh'=> \*DATA, '-format' => 'pfam' ); my $al = <$str>; # write out a MSF file my $out = Bio::AlignIO->newFh('-fh'=> \*STDOUT, '-format' => 'msf'); my $status = print $out $al; # order by alphabetically then start end $al->sort_alphabetically(); # write in Pfam format now... my $out2=Bio::AlignIO->newFh( '-fh'=> \*STDOUT, '-format' => 'pfam'); $status = print $out2 $al; # now set the display name to be # name_# like roa1_human_1, roa1_human_2 etc # This **doesn't** change the underlying names of the # sequences you'll be glad to hear. $al->set_displayname_count(); # dump again... bored of this yet? $status = print $out2 $al; # get into the alignment and get things out # we just want to see how many unique names # there are in this alignment my ($seq, $id, %hash) ; # loop over the alignment foreach $seq ( $al->eachSeq() ) { # increment a hash on the name by one each time $hash{$seq->id()}++; } # disgorge the hash foreach $id ( keys %hash ) { print "$id has $hash{$id} subsequences in this alignment\n"; } __END__ GR10_BRANA/8-79 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND.............RETGRSRGFGFVTFKDEKSMKDAIDEMNG.K...ELDGRTITV HUD_HUMAN/48-119 LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD.............KITGQSLGYGFVNYIDPKDAEKAINTLNG.L...RLQTKTIKV IF32_SCHPO/41-124 VVIEGAP....VVEEAKQQDFFRFLSSKVLAK.IGKVKENGFYMPFE.........EKNGK..KMSLGLVFADFENVDGADLCVQELDGKQ...ILKNHTFVV IF32_YEAST/79-157 IVVNGAPVIPSAKVPVLKKALTSLFS.....K.AGKV..VNMEFPID.............EATGKTKGFLFVECGSMNDAKKIIKSFHGKR...LDLKHRLFL IF4B_HUMAN/98-168 AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR............EPSNPERLKGFGYAEFEDLDSLLSALS.LNE.E...SLGNRRIRV LA_DROME/151-225 AYAKGF......PLDSQISELLDFTA.....N.YDKV..VNLTMRNS.........YDKPTKSYKFKGSIFLTFETKDQAKAFLE.QEK.I...VYKERELLR LA_HUMAN/113-182 VYIKGF......PTDATLDDIKEWLE.....D.KGQV..LNIQMRR..............TLHKAFKGSIFVVFDSIESAKKFVE.TPG.Q...KYKETDLLI MEI2_SCHPO/197-265 LFVTNL......PRIVPYATLLELFS.....K.LGDV..KGIDTSSL.................STDGICIVAFFDIRQAIQAAKSLRSQR...FFNDRLLYF MODU_DROME/177-246 VFVTNL......PNEYLHKDLVALFA.....K.FGRL..SALQRFTN................LNGNKSVLIAFDTSTGAEAVLQAKPKAL...TLGDNVLSV MODU_DROME/260-326 VVVGLI......GPNITKDDLKTFFE.....K.VAPV..EAVTISSN.................RLMPRAFVRLASVDDIPKALK.LHS.T...ELFSRFITV MODU_DROME/342-410 LVVENVG....KHESYSSDALEKIFK.....K.FGDV..EEIDVVC..................SKAVLAFVTFKQSDAATKALAQLDG.K...TVNKFEWKL MODU_DROME/422-484 ILVTNL......TSDATEADLRKVFN.....D.SGEI..ESIIMLG.....................QKAVVKFKDDEGFCKSFL.ANE.S...IVNNAPIFI MSSP_HUMAN/31-102 LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD.............KTTNKCKGYGFVDFDSPAAAQKAVSALKA.S...GVQAQKAKQ NAM8_YEAST/165-237 IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD.............QVTGMSKGYGFVKFTNSDEQQLALSEMQG.V...FLNGRAIKV NONA_DROME/304-369 LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD...................KNFTFLKVDYHPNAEKAKRALDG.S...MRKGRQLRV NONA_DROME/378-448 LRVSNL......TPFVSNELLYKSFE.....I.FGPI..ERASITVD..............DRGKHMGEGIVEFAKKSSASACLRMCNE.K...CFFLTASLR NOP3_YEAST/127-190 LFVRPF......PLDVQESELNEIFG.....P.FGPM..KEVKILN.....................GFAFVEFEEAESAAKAIEEVHG.K...SFANQPLEV NOP3_YEAST/202-270 ITMKNL......PEGCSWQDLKDLAR.....E.NSLE..TTFSSVN................TRDFDGTGALEFPSEEILVEALERLNN.I...EFRGSVITV NOP4_YEAST/28-98 LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD..............TNKRSRGFGFVSFAVEDDTKEALAKARK.T...KFNGHILRV NOP4_YEAST/292-363 VFVRNV......PYDATEESLAPHFS.....K.FGSV..KYALPVID.............KSTGLAKGTAFVAFKDQYTYNECIKNAPA.A...GSTSLLIGD NSR1_YEAST/170-241 IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE.............RGTDRSRGYGYVDFENKSYAEKAIQEMQG.K...EIDGRPINC NSR1_YEAST/269-340 LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH.............PETEQPKGFGYVQFSNMEDAKKALDALQG.E...YIDNRPVRL NUCL_CHICK/283-352 LFVKNL......TPTKDYEELRTAIK.....EFFGKK...NLQVSEV..............RIGSSKRFGYVDFLSAEDMDKALQ.LNG.K...KLMGLEIKL PABP_DROME/4-75 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD.............VITRRSLGYAYVNFQQPADAERALDTMNF.D...LVRNKPIRI PABP_DROME/92-162 VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD..............EKGNSKGYGFVHFETEEAANTSIDKVNG.M...LLNGKKVYV PABP_DROME/183-254 VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS..............KEDGKSKGFGFVAFETTEAAEAAVQALNGKD...MGEGKSLYV PABP_SCHPO/249-319 VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD..............QNDKPRGFGFVNYANHECAQKAVDELND.K...EYKGKKLYV PES4_YEAST/93-164 LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD.............SVTKKSLGHGYLNFEDKEEAEKAMEELNY.T...KVNGKEIRI PES4_YEAST/305-374 IFIKNL......PTITTRDDILNFFS.....E.VGPI..KSIYLSN...............ATKVKYLWAFVTYKNSSDSEKAIKRYNN.F...YFRGKKLLV PR24_YEAST/43-111 VLVKNL......PKSYNQNKVYKYFK.....H.CGPI..IHVDVAD...............SLKKNFRFARIEFARYDGALAAIT.KTH.K...VVGQNEIIV PR24_YEAST/119-190 LWMTNF......PPSYTQRNIRDLLQ.....D.INVV.ALSIRLPSL..............RFNTSRRFAYIDVTSKEDARYCVEKLNG.L...KIEGYTLVT PR24_YEAST/212-284 IMIRNL.....STELLDENLLRESFE.....G.FGSI..EKINIPAG............QKEHSFNNCCAFMVFENKDSAERALQ.MNR.S...LLGNREISV PSF_HUMAN/373-443 LSVRNL......SPYVSNELLEEAFS.....Q.FGPI..ERAVVIVD..............DRGRSTGKGIVEFASKPAARKAFERCSE.G...VFLLTTTPR PTB_HUMAN/61-128 IHIRKL......PIDVTEGEVISLGL.....P.FGKV..TNLLMLKG...................KNQAFIEMNTEEAANTMVN.YYT.SVTPVLRGQPIYI PTB_HUMAN/186-253 IIVENL......FYPVTLDVLHQIFS.....K.FGTV....LKIIT...............FTKNNQFQALLQYADPVSAQHAKLSLDG.Q...NIYNACCTL PUB1_YEAST/76-146 LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID..............KNNKNVNYAFVEYHQSHDANIALQTLNG.K...QIENNIVKI PUB1_YEAST/163-234 LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD.............MQTGSSRGYGFVSFTSQDDAQNAMDSMQG.Q...DLNGRPLRI PUB1_YEAST/342-407 AYIGNI......PHFATEADLIPLFQ.....N.FGFI..LDFKHYPE...................KGCCFIKYDTHEQAAVCIVALAN.F...PFQGRNLRT RB97_DROME/34-104 LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD.............AATKRSRGFGFITYTKSLMVDRAQE..NRPH...IIDGKTVEA RN12_YEAST/200-267 IVIKFQ......GPALTEEEIYSLFR.....R.YGTI....IDIFP...............PTAANNNVAKVRYRSFRGAISAKNCVSG.I...EIHNTVLHI RN15_YEAST/20-91 VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD.............PQTGRSKGYAFIEFRDLESSASAVRNLNG.Y...QLGSRFLKC RNP1_YEAST/37-109 LYVGNL......PKNCRKQDLRDLFE.....PNYGKI..TINMLKKK.............PLKKPLKRFAFIEFQEGVNLKKVKEKMNG.K...IFMNEKIVI RO28_NICSY/99-170 LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN.............RETDRSRGFGFVTMSTVEEADKAVELYSQ.Y...DLNGRLLTV RO33_NICSY/116-187 LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD.............RVTDRSRGFAFVTMGSVEEAKEAIRLFDG.S...QVGGRTVKV RO33_NICSY/219-290 LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD.............RSSGRSRGFGFITFSSAEAMNSALDTMNE.V...ELEGRPLRL ROA1_BOVIN/106-176 IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD.............RGSGKKRGFAFVTFDDHDSVDKIVI.QKY.H...TVNGHNCEV ROC_HUMAN/18-82 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK.....................GFAFVQYVNERNARAAVAGEDG.R...MIAGQVLDI ROF_HUMAN/113-183 VRLRGL......PFGCTKEEIVQFFS.....G.LEIV.PNGITLPVD..............PEGKITGEAFVQFASQELAEKALG.KHK.E...RIGHRYIEV ROG_HUMAN/10-81 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD.............RETNKSRGFAFVTFESPADAKDAARDMNG.K...SLDGKAIKV RT19_ARATH/33-104 LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN.............KVTGRSRGYGFVNFISEDSANSAISAMNG.Q...ELNGFNISV RU17_DROME/104-175 LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD.............QESGKPKGYAFIEYEHERDMHAAYKHADG.K...KIDSKRVLV RU1A_HUMAN/12-84 IYINNLNE..KIKKDELKKSLYAIFS.....Q.FGQI..LDILVSR................SLKMRGQAFVIFKEVSSATNALRSMQG.F...PFYDKPMRI RU1A_HUMAN/210-276 LFLTNL......PEETNELMLSMLFN.....Q.FPGF..KEVRLVPG..................RHDIAFVEFDNEVQAGAARDALQG.F...KITQNNAMK RU1A_YEAST/229-293 LLIQNL......PSGTTEQLLSQILG.....N.EALV...EIRLVSV...................RNLAFVEYETVADATKIKNQLGS.T...YKLQNNDVT RU2B_HUMAN/9-81 IYINNMND..KIKKEELKRSLYALFS.....Q.FGHV..VDIVALK................TMKMRGQAFVIFKELGSSTNALRQLQG.F...PFYGKPMRI RU2B_HUMAN/153-220 LFLNNL......PEETNEMMLSMLFN.....Q.FPGF..KEVRLVPG..................RHDIAFVEFENDGQAGAARDALQGFK...ITPSHAMKI SC35_CHICK/16-87 LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD.............RYTKESRGFAFVRFHDKRDAEDAMDAMDG.A...VLDGRELRV SP33_HUMAN/17-85 IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR................RGGPPFAFVEFEDPRDAEDAVYGRDG.Y...DYDGYRLRV SP33_HUMAN/122-186 VVVSGL......PPSGSWQDLKDHMR.....E.AGDV..CYADVYRD....................GTGVVEFVRKEDMTYAVRKLDN.T...KFRSHEGET SQD_DROME/58-128 LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD.............PQTGRSRGFAFIVFTNTEAIDKVSA.ADE.H...IINSKKVDP SQD_DROME/138-208 IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD.............KQKSQRKGFCFITFDSEQVVTDLLK.TPK.Q...KIAGKEVDV SR55_DROME/5-68 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN.....................GYGFVEFEDYRDADDAVYELNG.K...ELLGERVVV SSB1_YEAST/39-114 IFIGNV......AHECTEDDLKQLFV.....EEFGDE..VSVEIPIK..........EHTDGHIPASKHALVKFPTKIDFDNIKENYDT.K...VVKDREIHI SXLF_DROME/127-198 LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD.............YKTGYSFGYAFVDFTSEMDSQRAIKVLNG.I...TVRNKRLKV SXLF_DROME/213-285 LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD.............KLTGRPRGVAFVRYNKREEAQEAISALNNVI...PEGGSQPLS TIA1_HUMAN/9-78 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD...............TAGNDPYCFVEFHEHRHAAAALAAMNG.R...KIMGKEVKV TIA1_HUMAN/97-168 VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD.............MATGKSKGYGFVSFFNKWDAENAIQQMGG.Q...WLGGRQIRT TIA1_HUMAN/205-270 VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD...................KGYSFVRFNSHESAAHAIVSVNG.T...TIEGHVVKC TRA2_DROME/99-170 IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID.............AQTQRSRGFCFIYFEKLSDARAAKDSCSG.I...EVDGRRIRV U2AF_HUMAN/261-332 LFIGGL......PNYLNDDQVKELLT.....S.FGPL..KAFNLVKD.............SATGLSKGYAFCEYVDINVTDQAIAGLNG.M...QLGDKKLLV U2AF_SCHPO/312-383 IYISNL......PLNLGEDQVVELLK.....P.FGDL..LSFQLIKN.............IADGSSKGFCFCEFKNPSDAEVAISGLDG.K...DTYGNKLHA U2AG_HUMAN/67-142 CAVSDVEM..QEHYDEFFEEVFTEME.....EKYGEV..EEMNVCDN..............LGDHLVGNVYVKFRREEDAEKAVIDLNN.R...WFNGQPIHA WHI3_YEAST/540-614 LYVGNL......PSDATEQELRQLFS.....G.QEGF..RRLSFRNK..........NTTSNGHSHGPMCFVEFDDVSFATRALAELYG.R...QLPRSTVSS X16_HUMAN/12-78 VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN..................PPGFAFVEFEDPRDAADAVRELDG.R...TLCGCRVRV YHC4_YEAST/348-415 IFVGQL......DKETTREELNRRFS.....T.HGKI..QDINLIFK.................PTNIFAFIKYETEEAAAAALESENH.A...IFLNKTMHV YHH5_YEAST/315-384 ILVKNL......PSDTTQEEVLDYFS.....T.IGPI..KSVFISEK...............QANTPHKAFVTYKNEEESKKAQKCLNK.T...IFKNHTIWV YIS1_YEAST/66-136 IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD.............RNTGTPKGYGYIEFESPAYREKALQ.LNG.G...ELKGKKIAV YIS5_YEAST/33-104 IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD.............ENTGESQGFAYLKYEDQRSTILAVDNLNG.F...KIGGRALKI ARP2_PLAFA/364-438 VEVTYLF....STYLVNGQTL..IYS.....N.ISVV....LVILY........HQKFKETVLGRNSGFGFVSYDNVISAQHAIQFMNG.Y...FVNNKYLKV CABA_MOUSE/77-147 MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD.............PNTGRSRGFGFILFKDSSSVEKVLD.QKE.H...RLDGRVIDP CABA_MOUSE/161-231 IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID.............PKLNKRRGFVFITFKEEDPVKKVLE.KKF.H...TVSGSKCEI CPO_DROME/453-526 LFVSGL......PMDAKPRELYLLFR.....A.YEGY..EGSLLKV............TSKNGKTASPVGFVTFHTRAGAEAAKQDLQGVR...FDPDMPQTI CST2_HUMAN/18-89 VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD.............RETGKPKGYGFCEYQDQETALSAMRNLNG.R...EFSGRALRV D111_ARATH/281-360 LLLRNMVG.PGQVDDELEDEVGGECA.....K.YGTV..TRVLIFE..........ITEPNFPVHEAVRIFVQFSRPEETTKALVDLDG.R...YFGGRTVRA ELAV_DROME/250-322 LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN............AGNDTQTKGVGFIRFDKREEATRAIIALNG.T...TPSSCTDPI ELAV_DROME/404-475 IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD.............PTTNQCKGYGFVSMTNYDEAAMAIRALNG.Y...TMGNRVLQV EWS_HUMAN/363-442 IYVQGL......NDSVTLDDLADFFK.....Q.CGVV..K.MNKRTG....QPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG.K...DFQGSKLKV GBP2_YEAST/124-193 IFVRNL......TFDCTPEDLKELFG.....T.VGEV..VEADIIT...............SKGHHRGMGTVEFTKNESVQDAISKFDG.A...LFMDRKLMV GBP2_YEAST/221-291 VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD..............FNGFSRGFGSVIYPTEDEMIRAIDTFNG.M...EVEGRVLEV GBP2_YEAST/351-421 IYCSNL......PFSTARSDLFDLFG.....P.IGKI..NNAELKP..............QENGQPTGVAVVEYENLVDADFCIQKLNN.Y...NYGGCSLQI