fn3.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

FINC_BOVIN/1511-1590              KNGPGP.........SKTKT...VGPD....QT..EMTIEGLQPTVEYVV
FINC_BOVIN/875-955                VNLPGE........HGQRLP...VSRN....T...FAEVTGLSPGVTYHF
TENA_CHICK/593-671                TSSGGL.........DLQFT...VPGN....QT..SATIHELEPGVEYFI
FINC_BOVIN/1693-1771              ANGQT..........PIQRT...IRPD....VR..SYTITGLQPGTDYKI
FINC_BOVIN/1142-1225              TNGQQG........YSLEEV...VHAD....QS..SCTFENLSPGLEYNV
PTP1_DROME/405-485                TFNGD..........TSTLT...TDRT....R....FTLESLLPGRNYSL
FINC_BOVIN/1236-1316              VKNEED.........VAELS...ISPS....DN..AVVLTNLLPGTEYLV
PHB_ALCFA/344-418                 .NGS............KVGS...ATAT....A....YTDSGLIAGTTYSY
CHIX_STROI/169-240                .DGV............KVAT...ASGT....S....ATVTGLTPDTAYAF
CHIT_STRLI/142-219                .DGA............KVAT...VTGT....T....YTDNGLTKGTAYSY
GUNB_CELFI/651-733                QGTTQ..........TLVGT...TTAA....A....YILRDLTPGTAYSY
CHI1_BACCI/465-542                .GAN............LATS...VTGT....T....ATISGLTAGTSYTF
APU_THETY/1165-1248               SETGPF.........IKIAT...VSDS....VY..NYVDTDVVNGNVYYY
APU_THETY/928-1009                TVKGG..........LYEKI...ASNV....TQI.TYTDTEVTNGLKYVY
FINC_BOVIN/577-660                KNSPDR.........WKEAT...IPGH....LN..SYTIKGLRPGVVYEG
NRG_DROME/815-905                 ENEGEE........GLREIH...VKGD....TH..NALVTQFKPDSKNYA
PTP6_DROME/332-425                SGEVPKVI.....EEAIYQQ...NSRN....L...PYMFDKLKTATDYEF
FAS2_SCHAM/530-616                DSQGW..........EDALN...RTWP....VDS.PYILENLKPQTRYNF
PTPZ_HUMAN/312-401                LDGEDQ........TKHEFL...TDGY....QDL.GAILNNLLPNMSYVL
NCA1_BOVIN/610-691                LSSEW..........KPEIR...LPSG....SD..HVMLKSLDWNAEYEV
FAS2_SCHAM/642-735                VEKYDTEWRL.LPYPCQEHK...LEGQ....AT..TFQLESLQPDTHYKV
TIE2_HUMAN/543-626                VQKSD..........QQNIK...VPGN....LT..SVLLNNLHPREQYVV
TENA_CHICK/682-767                KDDNG..........DITSS...LKRP....ET..SYMQPGLAPGQQYNV
UFO_HUMAN/327-411                 QDTPE..........VLMDI...GLRQ....EV..TLELQGDGSVSNLTV
TIE1_HUMAN/545-632                GTRGQ..........ERREN...VSSP....QAR.TALLTGLTPGTHYQL
7LES_DROME/1799-1891              ELDGENVQD..RREWEAHER...RLET....AG..THRLTGIKPGSGYSL
NRG_DROME/717-799                 .RDIPAA......AWENNNI...FDWR....QN..NIVIADQPTFVKYLI
#=GR NRG_DROME/717-799    SS     .EEEEEE......SSSTTCC...EEEE....EE..EETTCSEEEEECCSS
#=GR NRG_DROME/717-799    SA     .001210......5245942...5425....67..044836215060213
NRCA_CHICK/726-810                DVDDE..........WTSVV...VANV....S...KYIVSGTPTFVPYEI
NGCA_CHICK/700-794                LEEPGGGGPS.GGFPWAEST...VDAP....P....VVVGGLPPFSPFQI
TIE2_HUMAN/639-724                QGKNE..........DQHVDV.KIKNA....TII.QYQLKGLEPETAYQV
LAR_DROME/515-598                 TYANQ..........AHHKR...ISNS....E...AYTLDGLYPDTLYYI
PTP6_DROME/236-321                AGTPTFT.......YHKDFI...NGSH....T...SYILDHFKPNTTYFL
TIE2_HUMAN/444-529                VNHYEA.........WQHIQ...VTNE....I....VTLNYLEPRTEYEL
TIE1_HUMAN/446-533                DSTMD..........WSTIV...VDPS....E...NVTLMNLRPKTGYSV
PTPK_MOUSE/290-376                T.SGS..........WTETH...AVNA....P...TYKLWHLDPDTEYEI
PTPB_HUMAN/1355-1434              MDTQEV.........EFSRK...LEKE....KS..LLNIMMLVPHKRYLV
PTP1_DROME/583-661                DSEQQ..........WVRLP...SVRS....T...EADITDMTKGEKYTI
PTP1_DROME/312-394                TRRQS..........TVPRS...NEPV....AF..SDFRDIAEPGKTFNV
PTP1_DROME/217-301                PDANDSVL.....YVEKEGE...PPGP....A...QAAFKGLVPGRAYNI
PTP1_DROME/123-205                LSEASSS.......YNRTFQ...VNDN....TF..QHSVKELTPGATYQV
PTPB_HUMAN/1261-1344              RDALTV.........FNPYN...NRKS....E...GRIVYGLRPGRSYQF
PTP1_DROME/864-944                A.DNL..........LAQNM...TTRN....E....ITISDLRPHRNYTF
PTPB_HUMAN/1173-1250              PNGTKK.........ENWKD...KDLT....E....WRFQGLVPGRKYVL
PTPB_HUMAN/1085-1162              PDGNLQ.........ERAQV...DPLV....Q...SFSFQNLLQGRMYKM
PTPB_HUMAN/467-543                R.DLL..........LIHKS...LSKD....AK..EFTFTDLVPGRKYMA
PTPB_HUMAN/995-1074               ENGIL..........LRNTS...EPAT....TK..QHKFEDLTPGKKYKI
PTPB_HUMAN/731-808                KNNF...........IQTKS...IPKS....EN..ECVFVQLVPGRLYSV
PTPB_HUMAN/643-725                DGKV...........VQSLV...IAKS....VR..ECSFSSLTPGRLYTV
PTPB_HUMAN/554-632                ENVV...........IKNES...ISSE....TS..RYSFHSLKSGSLYSV
PTPB_HUMAN/907-984                H.SQK..........VDSQT...IPKH....VF..EHTFHRLEAGEQYQI
PTPB_HUMAN/112-192                ENNQKIQ......GVQIQES...TSWN....E....YTFFNLTAGSKYNI
IL7R_HUMAN/129-221                KDENK..........WTHVN...LSST....KL..TLLQRKLQPAAMYEI
FINC_BOVIN/689-768                SEEGDE.........PQYLD...LPST....AT..SVNIPDLLPGRKYTV
KALM_CHICK/178-271                QGIHPSED.....DATNWQT...VAQT....TDE.RVQLSDIRASRWYQF
TENA_HUMAN/1529-1608              SGKLLD.........PQEFT...LSGT....QR..KLELRGLITGIGYEV
TENA_CHICK/1227-1306              KRKSD..........PLELI...VPGH....ER..THDITGLKEGTEYEI
TENA_CHICK/1136-1215              SNRLLE.........PMEFN...ISGN....SR..TAHISGLSPSTDFIV
TENA_HUMAN/1255-1335              ADQVEE.........AHNLT...VPGS....LR..SMEIPGLRAGTPYTV
TENA_CHICK/1045-1124              SDNPEE.........TWNIT...VPGG....QH..SVNVTGLKANTPYNV
7LES_DROVI/1917-1997              LREQ............LQFN...VAGN....HT..QMRLAPLQPKTRYSC
PTPB_HUMAN/22-103                 DTLGAA........LCPTFR...IDNT....TY..GCNLQDLQAGTIYNF
KALM_CHICK/544-642                VTTESRQNSLPNSIISQSQI...LPAD....HY..VLTVPNLRPSMLYRL
#=GC SS_cons                      CCCCCCEE.....CCCCCCE...EECC....CCC.CECECCEEEEECCCC
#=GC SA_cons                      44443434.....5355643...4336....563.233425323131333
#=GC seq_cons                     tsssp..........hpphs...lsss....p...phslssLpPsspYph

EPA1_HUMAN/333-435                NVE.AQNGVSGLGSSGHAS
EPA2_HUMAN/329-420                TVE.ARNGV........SG
EPA3_CHICK/325-421                EID.AVNGVSD...LSTLS
EPB2_CHICK/326-422                EIQ.AVNGVTD...QSPFS
NRCA_CHICK/623-709                RVI.AVNEIGR....SQPS
MYPF_CHICK/630-716                RVF.AVNAIGV....SQPS
MPSF_CHICK/801-887                KVR.AVNDAGV....GKSS
MPSF_CHICK/699-785                KIA.AANVVGI....GHPS
MPSF_CHICK/499-585                RVL.SANKHGI....SDPS
MPSF_CHICK/371-457                RVR.AVNSAGI....SRPS
KMLS_CHICK/1318-1403              RVR.AANVYGI....SEPS
AXO1_CHICK/602-692                RVL.ASNILGV....GEPS
MPSF_CHICK/600-684                RVK.AVNAVGF....SENS
LAR_DROME/322-404                 YVI.AVNNIGR....GPPS
MYPF_CHICK/923-1008               RVY.SENVCGT....SQEP
TIE1_HUMAN/644-729                RMR.ASI.QGL....GDWS
NCA1_BOVIN/509-597                RLA.ALNGKGL....GEIS
EPA4_MOUSE/441-525                HVR.ARTAAGY....GDFS
EPB2_CHICK/437-521                QVR.ARTVAGY....GRYS
NRCA_CHICK/928-1014               YFN.AQTSV......GSGS
LAR_DROME/909-995                 RVR.AYTKQGA....GPFS
ITB4_HUMAN/1641-1728              KVQ.ARTTEGF....GPER
ITB4_HUMAN/1528-1612              RVR.AQSQEGW....GRER
ITB4_HUMAN/1220-1310              TVK.ARNGAGW....GPER
#=GR ITB4_HUMAN/1220-1310 SS     CCC.CCCCCEE....ECCC
#=GR ITB4_HUMAN/1220-1310 SA     533.4135333....3234
PTP9_DROME/171-259                IVK.AFTTKNE....GEPS
LAR_DROME/709-800                 QVA.ALTRKGD....GDRS
LAR_DROME/417-503                 RVQ.AYTSMGA....GPMS
EPA2_HUMAN/436-519                QVQ.ALTQEGQ....GAGS
ITB4_HUMAN/1127-1208              KVC.AYGAQGE....GPYS
#=GR ITB4_HUMAN/1127-1208 SS     EEE.EEECTCC....CCCC
#=GR ITB4_HUMAN/1127-1208 SA     110.0115865....3341
CONT_CHICK/799-884                DVS.AFNSAGY....GPPS
AXO1_CHICK/807-896                SVR.AYNRAGA....GPPS
CAML_HUMAN/812-907                EVQ.AFNGRGS....GPAS
PTP1_DROME/958-1044               KIQ.AKTAIGF....GPER
NRG_DROME/917-1007                SIT.ATTKMGE....GSEH
TENA_CHICK/1494-1571              KLQ.ALSRS.......MRS
TENA_CHICK/956-1033               SLV.AEKGR.......HKS
TENA_CHICK/1406-1483              RVH.AVKDA.......QKS
TENA_CHICK/774-853                TLI.SRRGD.......MES
TENA_CHICK/1317-1395              NII.SVKGF.......EES
FINC_BOVIN/1327-1406              SIV.ALNSK.......EES
FINC_RAT/1266-1346                SVI.TLING.......GES
TENA_CHICK/864-945                GVT.AVRQD.......RES
FINC_BOVIN/780-858                TIY.AVEEN.......QES
FINC_BOVIN/1782-1861              QVI.ALKNN.......QKS
FINC_BOVIN/1417-1499              TVY.AVTGRGD....SPAS
FINC_BOVIN/1601-1680              SVY.ALKDT.......LTS
FINC_BOVIN/1511-1590              SVY.AQNQN.......GES
FINC_BOVIN/875-955                KVF.AVNQG.......RES
TENA_CHICK/593-671                RVF.AILKN.......KKS
FINC_BOVIN/1693-1771              HLY.TLNDN.......ARS
FINC_BOVIN/1142-1225              SVY.TVKDD.......KES
PTP1_DROME/405-485                SVQ.AVSKK.......MES
FINC_BOVIN/1236-1316              SVS.SVYEQ.......HES
PHB_ALCFA/344-418                 TVT.AVDPTAG...ESQPS
CHIX_STROI/169-240                QVA.AVNGA.......GES
CHIT_STRLI/142-219                SVK.ARDTADQ...TGPAS
GUNB_CELFI/651-733                VVK.AKDVAGN...VSAAS
CHI1_BACCI/465-542                TIK.AKDAAGN...LSAAS
APU_THETY/1165-1248               KVV.AVDTSYN....RTAS
APU_THETY/928-1009                AVT.AVDNDGN...ESALS
FINC_BOVIN/577-660                QLI.SVQHY......GQRE
NRG_DROME/815-905                 RIL.AYNGRFN....GPPS
PTP6_DROME/332-425                RVR.ACSDLTKT..CGPWS
FAS2_SCHAM/530-616                RFA.AQNEVGF....GPWS
PTPZ_HUMAN/312-401                QIV.AICTNGL...YGKYS
NCA1_BOVIN/610-691                YVV.AENQQ.......GKS
FAS2_SCHAM/642-735                EVR.ATNAIGN....SVPG
TIE2_HUMAN/543-626                RAR..VNTKAQ....GEWS
TENA_CHICK/682-767                SLH.IVKNNTR...GPGLS
UFO_HUMAN/327-411                 CVA.AYTAAGD....GPWS
TIE1_HUMAN/545-632                DVQ.LYHCTLL....GPAS
7LES_DROME/1799-1891              WVQ.AHATPTK....SNSS
NRG_DROME/717-799                 KVV.AINDR.......GES
#=GR NRG_DROME/717-799    SS     EEE.EEEEE.......EEE
#=GR NRG_DROME/717-799    SA     030.10200.......020
NRCA_CHICK/726-810                KVQ.ALNDLGY...APEPS
NGCA_CHICK/700-794                RVQ.AVNGAGK....GPEA
TIE2_HUMAN/639-724                DIF.AENNIGS....SNPA
LAR_DROME/515-598                 WLA.ARSQRGE....GATT
PTP6_DROME/236-321                RIV.GKNSIGN....GQPT
TIE2_HUMAN/444-529                CVQ.LVRRGEG....GEGH
TIE1_HUMAN/446-533                RVQLSRPGEGG...EGAWG
PTPK_MOUSE/290-376                RVLLTRPGEGG...TGLPG
PTPB_HUMAN/1355-1434              SIK.VQSAG.......MTS
PTP1_DROME/583-661                QVN.TVSFG.......VES
PTP1_DROME/312-394                IVK.TVSGK.......VTS
PTP1_DROME/217-301                SVQ.TMSED.......EIS
PTP1_DROME/123-205                QAY.TIYDG.......KES
PTPB_HUMAN/1261-1344              NVK.TVSGDSW....KTYS
PTP1_DROME/864-944                TVV.VRSGTESS..VLRSS
PTPB_HUMAN/1173-1250              WVV.THSGD........LS
PTPB_HUMAN/1085-1162              VIV.THSGE........LS
PTPB_HUMAN/467-543                TVT.SISGD........LK
PTPB_HUMAN/995-1074               QIL.TVSGG.......LFS
PTPB_HUMAN/731-808                TVT.TKSGQ........YE
PTPB_HUMAN/643-725                TIT.TRSGKYE...NHSFS
PTPB_HUMAN/554-632                VVT.TVSGG.......ISS
PTPB_HUMAN/907-984                MIA.SVSGS........LK
PTPB_HUMAN/112-192                AIT.AVSGG.......KRS
IL7R_HUMAN/129-221                KVR.SIPDHYFKGFWSEWS
FINC_BOVIN/689-768                NVY.EISEE.......GEQ
KALM_CHICK/178-271                RVA.AVNVHGT...RGFTA
TENA_HUMAN/1529-1608              MVS.GFTQG.......HQT
TENA_CHICK/1227-1306              ELY.GVSSG.......RRS
TENA_CHICK/1136-1215              YLY.GISHG.......FRT
TENA_HUMAN/1255-1335              TLH.GEVRG.......HST
TENA_CHICK/1045-1124              TLY.GVIRG.......YRT
7LES_DROVI/1917-1997              RLA.LAYAATP....GAPI
PTPB_HUMAN/22-103                 KII.SLDEE........RT
KALM_CHICK/544-642                EVQ.VLTTGGE....GPAT
#=GC SS_cons                      EEE.EEECCCC....CCCC
#=GC SA_cons                      221.2123454....3232
#=GC seq_cons                     pVt.Ahsst.......t.S
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