rrm.sto

这是一个基于HMM 模型的生物多序列比对算法的linux实现版本。hmmer

# STOCKHOLM 1.0



YIS5_YEAST/33-104               IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD...
YIS1_YEAST/66-136               IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD...
RN15_YEAST/20-91                VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD...
CST2_HUMAN/18-89                VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD...
NSR1_YEAST/269-340              LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH...
IF4B_HUMAN/98-168               AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR....
TIA1_HUMAN/108-179              VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD...
PUB1_YEAST/163-234              LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD...
NAM8_YEAST/165-237              IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD...
RT19_ARATH/33-104               LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN...
NSR1_YEAST/170-241              IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE...
PES4_YEAST/93-164               LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD...
PABP_DROME/4-75                 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD...
NOP4_YEAST/28-98                LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD...
ROC5_NICSY/219-290              LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD...
ROC5_NICSY/116-187              LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD...
ROC3_NICSY/99-170               LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN...
GBP2_YEAST/221-291              VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD...
PABP_SCHPO/263-333              VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD...
PABP_DROME/183-254              VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS....
PABP_DROME/92-162               VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD...
SFR3_HUMAN/12-78                VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN...
SR55_DROME/5-68                 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN....
SFR1_HUMAN/17-85                IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR...
SFR2_CHICK/16-87                LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD...
ROG_HUMAN/10-81                 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD...
TRA2_DROME/99-170               IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID...
ROC_HUMAN/18-82                 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK....
NONA_DROME/304-369              LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD...
RU17_DROME/104-175              LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD...
TIA1_HUMAN/216-281              VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD...
TIA1_HUMAN/9-78                 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD...
PUB1_YEAST/76-146               LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID...
SXL_DROME/213-285               LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD...
ELAV_DROME/250-322              LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN...
SXL_DROME/127-198               LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD...
ELV4_HUMAN/48-119               LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD...
MSSP_HUMAN/31-102               LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD...
ELAV_DROME/404-475              IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD...
SQD_DROME/138-208               IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD...
ROA1_BOVIN/106-176              IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD...
CABA_MOUSE/161-231              IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID...
SQD_DROME/58-128                LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD...
RB97_DROME/34-104               LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD...
GR10_BRANA/8-79                 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND...
CABA_MOUSE/77-147               MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD...
SFPQ_HUMAN/373-443              LSVRNL......SPYVSNELLEEAFS.....Q.FGPI..ERAVVIVD...
NONA_DROME/378-448              LRVSNL......TPFVSNELLYKSFE.....I.FGPI..ERASITVD...
NOP3_YEAST/127-190              LFVRPF......PLDVQESELNEIFG.....P.FGPM..KEVKILN....
GBP2_YEAST/124-193              IFVRNL......TFDCTPEDLKELFG.....T.VGEV..VEADIIT....
U2AF_SCHPO/312-383              IYISNL......PLNLGEDQVVELLK.....P.FGDL..LSFQLIKN...
U2AF_HUMAN/261-332              LFIGGL......PNYLNDDQVKELLT.....S.FGPL..KAFNLVKD...
NUCL_CHICK/283-352              LFVKNL......TPTKDYEELRTAIK.....EFFGKK...NLQVSEV...
MODU_DROME/342-410              LVVENVG....KHESYSSDALEKIFK.....K.FGDV..EEIDVVC....
RU2B_HUMAN/9-81                 IYINNMND..KIKKEELKRSLYALFS.....Q.FGHV..VDIVALK....
RU1A_HUMAN/12-84                IYINNLNE..KIKKDELKKSLYAIFS.....Q.FGQI..LDILVSR....
PUB1_YEAST/342-407              AYIGNI......PHFATEADLIPLFQ.....N.FGFI..LDFKHYPE...
PTB_HUMAN/186-253               IIVENL......FYPVTLDVLHQIFS.....K.FGTV....LKIIT....
EWS_HUMAN/363-442               IYVQGL......NDSVTLDDLADFFK.....Q.CGVV..K.MNKRTGQPM
ARP2_PLAFA/364-438              VEVTYLF....STYLVNGQTL..IYS.....N.ISVV....LVILY....
YHH5_YEAST/315-384              ILVKNL......PSDTTQEEVLDYFS.....T.IGPI..KSVFISEK...
PES4_YEAST/305-374              IFIKNL......PTITTRDDILNFFS.....E.VGPI..KSIYLSN....
YHC4_YEAST/348-415              IFVGQL......DKETTREELNRRFS.....T.HGKI..QDINLIFK...
PR24_YEAST/212-284              IMIRNL.....STELLDENLLRESFE.....G.FGSI..EKINIPAG...
MODU_DROME/422-484              ILVTNL......TSDATEADLRKVFN.....D.SGEI..ESIIMLG....
RNP1_YEAST/37-109               LYVGNL......PKNCRKQDLRDLFE.....PNYGKI..TINMLKKK...
GBP2_YEAST/351-421              IYCSNL......PFSTARSDLFDLFG.....P.IGKI..NNAELKP....
NOP4_YEAST/292-363              VFVRNV......PYDATEESLAPHFS.....K.FGSV..KYALPVID...
MEI2_SCHPO/197-265              LFVTNL......PRIVPYATLLELFS.....K.LGDV..KGIDTSSL...
IF39_YEAST/79-157               IVVNGAPVIPSAKVPVLKKALTSLFS.....K.AGKV..VNMEFPID...
ROF_HUMAN/113-183               VRLRGL......PFGCTKEEIVQFFS.....G.LEIV.PNGITLPVD...
MODU_DROME/260-326              VVVGLI......GPNITKDDLKTFFE.....K.VAPV..EAVTISSN...
WHI3_YEAST/540-614              LYVGNL......PSDATEQELRQLFS.....G.QEGF..RRLSFRNK...
CPO_DROME/453-526               LFVSGL......PMDAKPRELYLLFR.....A.YEGY..EGSLLKV....
RU2B_HUMAN/153-220              LFLNNL......PEETNEMMLSMLFN.....Q.FPGF..KEVRLVPG...
RU1A_HUMAN/210-276              LFLTNL......PEETNELMLSMLFN.....Q.FPGF..KEVRLVPG...
RU1A_YEAST/229-293              LLIQNL......PSGTTEQLLSQILG.....N.EALV...EIRLVSV...
SFR1_HUMAN/122-186              VVVSGL......PPSGSWQDLKDHMR.....E.AGDV..CYADVYRD...
NOP3_YEAST/202-270              ITMKNL......PEGCSWQDLKDLAR.....E.NSLE..TTFSSVN....
U2AG_HUMAN/67-142               CAVSDVEM..QEHYDEFFEEVFTEME.....EKYGEV..EEMNVCDN...
D111_ARATH/285-364              LLLRNMVG.PGQVDDELEDEVGGECG.....K.YGTV..TRVLIFE....
PR24_YEAST/43-111               VLVKNL......PKSYNQNKVYKYFK.....H.CGPI..IHVDVAD....
MODU_DROME/177-246              VFVTNL......PNEYLHKDLVALFA.....K.FGRL..SALQRFTN...
SSB1_YEAST/39-114               IFIGNV......AHECTEDDLKQLFV.....EEFGDE..VSVEIPIK...
RN12_YEAST/200-267              IVIKFQ......GPALTEEEIYSLFR.....R.YGTI....IDIFP....
PTB_HUMAN/61-128                IHIRKL......PIDVTEGEVISLGL.....P.FGKV..TNLLMLKG...
LA_HUMAN/113-182                VYIKGF......PTDATLDDIKEWLE.....D.KGQV..LNIQMRR....
LA_DROME/151-225                AYAKGF......PLDSQISELLDFAA.....N.YDKV..VNLTMRK....
PR24_YEAST/119-190              LWMTNF......PPSYTQRNIRDLLQ.....D.INVV.ALSIRLPSL...
IF39_SCHPO/41-124               VVIEGAP....VVEEAKQQDFFRFLSSKVLAK.IGKVKENGFYMPFE...

YIS5_YEAST/33-104               ......ENTGESQGF.....AYLKYEDQRSTILAVDNLNG.F...KIGGR
YIS1_YEAST/66-136               ......RNTGTPKGY.....GYIEFESPAYREKALQ.LNG.G...ELKGK
RN15_YEAST/20-91                ......PQTGRSKGY.....AFIEFRDLESSASAVRNLNG.Y...QLGSR
CST2_HUMAN/18-89                ......RETGKPKGY.....GFCEYQDQETALSAMRNLNG.R...EFSGR
NSR1_YEAST/269-340              ......PETEQPKGF.....GYVQFSNMEDAKKALDALQG.E...YIDNR
IF4B_HUMAN/98-168               ....EPSNPERLKGF.....GYAEFEDLDSLLSALS.LNE.E...SLGNR
TIA1_HUMAN/108-179              ......MATGKSKGY.....GFVSFFNKWDAENAIQQMGG.Q...WLGGR
PUB1_YEAST/163-234              ......MQTGSSRGY.....GFVSFTSQDDAQNAMDSMQG.Q...DLNGR
NAM8_YEAST/165-237              ......QVTGMSKGY.....GFVKFTNSDEQQLALSEMQG.V...FLNGR
RT19_ARATH/33-104               ......KVTGRSRGY.....GFVNFISEDSANSAISAMNG.Q...ELNGF
NSR1_YEAST/170-241              ......RGTDRSRGY.....GYVDFENKSYAEKAIQEMQG.K...EIDGR
PES4_YEAST/93-164               ......SVTKKSLGH.....GYLNFEDKEEAEKAMEELNY.T...KVNGK
PABP_DROME/4-75                 ......VITRRSLGY.....AYVNFQQPADAERALDTMNF.D...LVRNK
NOP4_YEAST/28-98                .......TNKRSRGF.....GFVSFAVEDDTKEALAKARK.T...KFNGH
ROC5_NICSY/219-290              ......RSSGRSRGF.....GFITFSSAEAMNSALDTMNE.V...ELEGR
ROC5_NICSY/116-187              ......RVTDRSRGF.....AFVTMGSVEEAKEAIRLFDG.S...QVGGR
ROC3_NICSY/99-170               ......RETDRSRGF.....GFVTMSTVEEADKAVELYSQ.Y...DLNGR
GBP2_YEAST/221-291              .......FNGFSRGF.....GSVIYPTEDEMIRAIDTFNG.M...EVEGR
PABP_SCHPO/263-333              .......QNDKPRGF.....GFVNYANHECAQKAVDELND.K...EYKGK
PABP_DROME/183-254              ......KEDGKSKGF.....GFVAFETTEAAEAAVQALNGKD...MGEGK
PABP_DROME/92-162               .......EKGNSKGY.....GFVHFETEEAANTSIDKVNG.M...LLNGK
SFR3_HUMAN/12-78                ...........PPGF.....AFVEFEDPRDAADAVRELDG.R...TLCGC
SR55_DROME/5-68                 .............GY.....GFVEFEDYRDADDAVYELNG.K...ELLGE
SFR1_HUMAN/17-85                .........RGGPPF.....AFVEFEDPRDAEDAVYGRDG.Y...DYDGY
SFR2_CHICK/16-87                ......RYTKESRGF.....AFVRFHDKRDAEDAMDAMDG.A...VLDGR
ROG_HUMAN/10-81                 ......RETNKSRGF.....AFVTFESPADAKDAARDMNG.K...SLDGK
TRA2_DROME/99-170               ......AQTQRSRGF.....CFIYFEKLSDARAAKDSCSG.I...EVDGR
ROC_HUMAN/18-82                 .............GF.....AFVQYVNERNARAAVAGEDG.R...MIAGQ
NONA_DROME/304-369              ............KNF.....TFLKVDYHPNAEKAKRALDG.S...MRKGR
RU17_DROME/104-175              ......QESGKPKGY.....AFIEYEHERDMHAAYKHADG.K...KIDSK
TIA1_HUMAN/216-281              ............KGY.....SFVRFNSHESAAHAIVSVNG.T...TIEGH
TIA1_HUMAN/9-78                 ........TAGNDPY.....CFVEFHEHRHAAAALAAMNG.R...KIMGK
PUB1_YEAST/76-146               .......KNNKNVNY.....AFVEYHQSHDANIALQTLNG.K...QIENN
SXL_DROME/213-285               ......KLTGRPRGV.....AFVRYNKREEAQEAISALNNVI...PEGGS
ELAV_DROME/250-322              .....AGNDTQTKGV.....GFIRFDKREEATRAIIALNG.T...TPSSC
SXL_DROME/127-198               ......YKTGYSFGY.....AFVDFTSEMDSQRAIKVLNG.I...TVRNK
ELV4_HUMAN/48-119               ......KITGQSLGY.....GFVNYIDPKDAEKAINTLNG.L...RLQTK
MSSP_HUMAN/31-102               ......KTTNKCKGY.....GFVDFDSPAAAQKAVSALKA.S...GVQAQ
ELAV_DROME/404-475              ......PTTNQCKGY.....GFVSMTNYDEAAMAIRALNG.Y...TMGNR
SQD_DROME/138-208               ......KQKSQRKGF.....CFITFDSEQVVTDLLK.TPK.Q...KIAGK
ROA1_BOVIN/106-176              ......RGSGKKRGF.....AFVTFDDHDSVDKIVI.QKY.H...TVNGH
CABA_MOUSE/161-231              ......PKLNKRRGF.....VFITFKEEDPVKKVLE.KKF.H...TVSGS
SQD_DROME/58-128                ......PQTGRSRGF.....AFIVFTNTEAIDKVSA.ADE.H...IINSK
RB97_DROME/34-104               ......AATKRSRGF.....GFITYTKSLMVDRAQE..NRPH...IIDGK