
                                 ehmmpfam 



Function

   Align single sequence with an HMM

Description

   **************** EDIT HERE ****************

Algorithm

   **************** EDIT HERE ****************

Usage

   Here is a sample session with ehmmpfam


% ehmmpfam 7LES_DROME ../ehmm-own-keep/myhmms 
Align single sequence with an HMM
Output file [7les_drome.ehmmpfam]: 

                CS    PSPPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGENV
                RF    PSPPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGENV
                   *->PsaPpnlsvtevtstsillsWwppdpggggyivyyvysegggdeeee
                      Ps+P+n sv   ++  + +sW pp+   ++ ++y +++++++d e++
  7LES_DROME  1799    PSPPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGENV 1845

                CS QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH
                RF QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH
                   ttpstsnttttllllllltytvyvvvvvsasssggsg<-*
                    ++++ + ++++l + ++   + +   +++s +  +
  7LES_DROME  1846 QDRREWEAHERRLETAGTHRLTGIKPGSGYSLWVQAH    1882

                CS    LKLLRFLGSGAFGEVYEGQLKTEDSEEPQRVAIKSLRKGASEFAELL
                RF    LKLLRFLGSGAFGEVYEGQLKTEDSEEPQRVAIKSLRKGASEFAELL
                   *->yelgekLGeGafGkVykakhkdtgkavaiKvikkekekekeeeteer
                      ++l++ LG+GafG+Vy++++k ++ +  + v++k+ +k   e +e +
  7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTEDSEEPQRVAIKSLRKGASEFAELL 2255

                CS QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAARATS
                RF QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAARATS
                   elrllknllhlniiilsehieytldlllllmellellllllllklrlvls
                   ++++l+++ ++++i++++ i ++++++ l+me +e ++ll++l++ +++s
  7LES_DROME  2256 QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAARATS 2305

                CS TQEPQPTAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTEST
                RF TQEPQPTAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTEST
                   elviaatliallliylllhhhlhidrkdlldlllldnlllikdidladlv
                    ++   t    l + l +++ +   +  l+d+++++++l++ + +++ +
  7LES_DROME  2306 TQEPQPTAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTEST 2355

                CS GSTDRRRTVKIGDFGLARDIYKSDYYRKEGEGLLPVRWMSPESLVDGLFT
                RF GSTDRRRTVKIGDFGLARDIYKSDYYRKEGEGLLPVRWMSPESLVDGLFT
                   llgsstltkkttstgtyrapevlageyssssslsssevlslevllilllg
                   +++++ +t k++++g  r +++ +++ +++++l +++++s+e+l + l++
  7LES_DROME  2356 GSTDRRRTVKIGDFGLARDIYKSDYYRKEGEGLLPVRWMSPESLVDGLFT 2405

                CS TQSDVWAFGVLCWEILTLGQQPYAARNNFEVLAHVKEGGRLQQPPMCTEK
                RF TQSDVWAFGVLCWEILTLGQQPYAARNNFEVLAHVKEGGRLQQPPMCTEK
                   tplgslldekllliildlifdpprpspleelsedlskllplplklrkpll
                   t  ++++++ l ++il+l+++p+  +++ e+  +++  ++l+++++++++
  7LES_DROME  2406 TQSDVWAFGVLCWEILTLGQQPYAARNNFEVLAHVKEGGRLQQPPMCTEK 2455

                CS LYSLLLLCWRTDPWERPSFRR
                RF LYSLLLLCWRTDPWERPSFRR
                   lllplrlnplskllallsplk<-*
                   l   l l ++++++ ++s+++
  7LES_DROME  2456 LYSLLLLCWRTDPWERPSFRR    2476


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-hmmfile]           infile     HMM file
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -nucleic            boolean    Force nucleic comparison
   -nalign             integer    Number of alignments
   -evalue             float      E-value cutoff
   -hitcut             float      Hit score cutoff
   -dbsize             integer    Calc E-value for DB size n
   -cpu                integer    Number of CPUs
   -dome               float      E-value domain cutoff
   -domt               float      Hit score domain cutoff
   -forward            boolean    Use forward algorithm
   -nulltwo            boolean    Turn off second null model
   -pvm                boolean    Use parallel virtual machine
   -xnu                boolean    Use XNU filtering

   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-hmmfile]
   (Parameter 2) HMM file Input file Required
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.ehmmpfam
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -nucleic Force nucleic comparison Boolean value Yes/No No
   -nalign Number of alignments Any integer value 100
   -evalue E-value cutoff Any numeric value 10.
   -hitcut Hit score cutoff Any numeric value -1000000.
   -dbsize Calc E-value for DB size n Any integer value 59021
   -cpu Number of CPUs Any integer value 0
   -dome E-value domain cutoff Any numeric value 1000000.
   -domt Hit score domain cutoff Any numeric value -1000000.
   -forward Use forward algorithm Boolean value Yes/No No
   -nulltwo Turn off second null model Boolean value Yes/No No
   -pvm Use parallel virtual machine Boolean value Yes/No No
   -xnu Use XNU filtering Boolean value Yes/No No

Input file format

   ehmmpfam reads any normal sequence USAs.

  Input files for usage example

  File: 7LES_DROME

ID   7LES_DROME     STANDARD;      PRT;  2554 AA.
AC   P13368;
DT   01-JAN-1990 (REL. 13, CREATED)
DT   01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)
DT   01-NOV-1995 (REL. 32, LAST ANNOTATION UPDATE)
DE   SEVENLESS PROTEIN (EC 2.7.1.112).
GN   SEV.
OS   DROSOPHILA MELANOGASTER (FRUIT FLY).
OC   EUKARYOTA; METAZOA; ARTHROPODA; INSECTA; DIPTERA.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=CANTON-S;
RX   MEDLINE; 88282538.
RA   BASLER K., HAFEN E.;
RL   CELL 54:299-311(1988).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   STRAIN=OREGON-R;
RX   MEDLINE; 88329706.
RA   BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
RL   GENES DEV. 2:620-634(1988).
RN   [3]
RP   IDENTIFICATION OF FN-III REPEATS.
RX   MEDLINE; 90199889.
RA   NORTON P.A., HYNES R.O., RESS D.J.G.;
RL   CELL 61:15-16(1990).
CC   -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
CC       INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
CC       LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
CC       SURFACE OF THE NEIGHBORING R8 CELL.
CC   -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
CC       PROTEIN TYROSINE PHOSPHATE.
CC   -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
CC   -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
CC       PROTEIN KINASES.
CC   -!- SIMILARITY: CONTAINS SEVEN FIBRONECTIN TYPE III-LIKE DOMAINS.
CC   -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
CC       NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
CC       NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
DR   EMBL; X13666; G8579; ALT_INIT.
DR   EMBL; J03158; G158419; -.
DR   PIR; A28912; TVFF7L.
DR   FLYBASE; FBGN0003366; SEV.
DR   PROSITE; PS00107; PROTEIN_KINASE_ATP.
DR   PROSITE; PS00109; PROTEIN_KINASE_TYR.
DR   PROSITE; PS00239; RECEPTOR_TYR_KIN_II.
DR   PROSITE; PS50011; PROTEIN_KINASE_DOM.
KW   TRANSFERASE; TYROSINE-PROTEIN KINASE; TRANSMEMBRANE; ATP-BINDING;
KW   PHOSPHORYLATION; RECEPTOR; VISION; REPEAT.
FT   DOMAIN        1   2123       EXTRACELLULAR (POTENTIAL).


  [Part of this file has been deleted for brevity]

FT   VARIANT    1703   1703       N -> H.
FT   VARIANT    1730   1730       R -> K.
FT   VARIANT    1731   1731       G -> E.
FT   VARIANT    1741   1741       V -> M.
FT   VARIANT    2271   2271       R -> C.
FT   CONFLICT   1823   1823       E -> Q (IN REF. 2).
SQ   SEQUENCE   2554 AA;  287107 MW;  1143D891 CRC32;
     MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
     SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
     CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
     SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
     KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
     QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
     LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
     LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
     NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
     TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
     SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
     ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
     QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
     SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
     KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
     VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
     PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
     CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
     GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
     PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
     VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
     AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
     DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
     TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
     EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
     RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
     GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
     DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
     LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
     VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
     PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
     AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
     GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
     GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
     RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
     HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
     LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
     GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
     SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
     HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
     DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
     LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
     HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
//

  File: ../ehmm-own-keep/myhmms

HMMER2.0
NAME  7LES_DROME/1799-1891
ACC
DESC
LENG  84
ALPH  Amino
RF    yes
CS    yes
MAP   yes
COM   ehmmbuild ../../data/hmm/fn3.slx fn3.hmm
COM   ehmmcalibrate myhmms -seed 1079460101
NSEQ  109
DATE  Fri Feb 18 09:57:19 2005
CKSUM 4633
XT      -8455     -4      0      *  -8455     -4      0      *
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1
085   -142    -21   -313     45    531    201    384  -1998   -644
EVD    -7.797886   0.598186
HMM        A      C      D      E      F      G      H      I      K      L
  M      N      P      Q      R      S      T      V      W      Y
         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
          -13      *  -6794
     1  -1696  -4266  -5468   -857  -4249  -2813  -1464   -707  -2361    323  -
3458  -4826   3646  -1897  -4829  -1261  -1335   -180  -4697  -1445     1
     P   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     P     -9 -11957 -12999   -894  -1115   -701  -1378  -1013  -7375
     2   -661  -5430   1594   -484  -5749    356  -3594  -5499  -1902   -454  -
4519   -541   1746  -1534  -3682   1881   -218  -1175  -5614  -1565     2
     S   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     S     -9 -11957 -12999   -894  -1115   -701  -1378  -7388  -7366
     3   1863  -5433  -1246     26  -5754   -787  -3592  -5505    174  -2261  -
4522   -578   2069    517    -53    117   -885   -568  -5616  -1862     3
     P   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     P     -9 -11957 -12999   -894  -1115   -701  -1378  -7388  -7358
     4   -933  -4330  -2306  -2375  -4321  -5548  -4342   -197  -4555  -1694  -
3520  -1961   3679  -1767  -2193  -4571  -2165   1336  -4755  -4362     4
     P   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     P     -9 -11957 -12999   -894  -1115   -701  -1378  -7388  -7349
     5  -1820  -5403  -2308    327   -457    168   -395  -1516   -104   -520
-384  -3583   1306   1270   1192    730    882  -1087  -5594  -1860     5
     R   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     R     -9 -11957 -12999   -894  -1115   -701  -1378  -7388  -7340
     6   -982   -749   1190  -1011  -1118   1264   -288   -624   -762  -1316  -
4520   2373  -1293    508    144  -1253    226  -5052   -320  -1913     6
     N   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     N     -9 -11957 -12999   -894  -1115   -701  -1378  -7388  -7331
     7   -970  -4169   -164   -707    -29  -1178  -4516    340  -5043   1932
 627    101    392   -968  -2232  -4736  -2233   1416  -4614  -4253     7
     F   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     F    -10 -11957 -12999   -894  -1115   -701  -1378  -7388  -7322
     8  -1777  -5430  -1395   -133   -485  -1202   1638   -150    523   -314  -
4519  -1070   -385    709   1029    806    906    500  -5614  -4932     8
     S   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     S    -10 -11957 -12999   -894  -1115   -701  -1378  -7388  -7313
     9   1184    673  -6214  -5601   1588  -1269   -129    561   -975  -1205  -
1064  -2147  -1311    219   -852   -479     57   1890  -4575  -4223     9
     V   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     V    -10 -11957 -12999   -894  -1115   -701  -1378  -7388  -7304
    10   -618  -1044   -126    168  -1034  -1670  -1237   -302    -47   -169
 624   -828  -5103   -865   -727   1021   1874    314    666  -1660    10
     R   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249


  [Part of this file has been deleted for brevity]

     V   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     V    -17 -11290 -12332   -894  -1115   -701  -1378  -7171  -6443
    57    415   -235    151  -1692    196   -943  -3424   1368   -281    543
1497  -1265  -4765   1123   -714  -1118   -698    331  -4311    -27    57
     L   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     L    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6426
    58   -392  -4801   1422    154    257   -976   -325   -348   1136   -182
-518   -449   -582     84   1071    -42   -259  -4422  -4984  -1114    58
     D   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     D    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6409
    59   1019   -244   -720    268   -486   -304   -511   -857   -597    384  -
3883   1880  -1432     25   -266   -599    544  -1258  -4979  -4298    59
     Q   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     Q    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6392
    60   -648   -361  -1645    149  -1712    -98  -2976    195    284    942
2156   1642  -1798    637   -685   -614  -1393  -4368  -4953   -253    60
     K   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     K    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6375
    61   -495   -127    596    257      1    687   -344  -4870    388  -1674
 888   2158   -252    554   -557  -1192   -645   -925  -4984  -1289    61
     E   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     E    -18 -11291 -12333   -894  -1115   -701  -1378  -7171  -6358
    62  -1174  -4786   -513    345   -470   1975   1744  -1919    674   -976
 236    503  -2145    935  -1306  -3214  -1546   -956  -4974    781    62
     H   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     H    -19 -11292 -12334   -894  -1115   -701  -1378  -7171  -6340
    63   -666   -120    197    263    443    569  -3004    492    662   -346
-777    690  -4431    450   -205   -417   -479    105  -4895    226    63
     R   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     R    -19 -11292 -12334   -894  -1115   -701  -1378  -7171  -6322
    64  -1695  -4564     90    808    321   -207   -958    170    606   -195
1319  -1668  -4468     42    233  -1958   -348    952   -101   1161    64
     L   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     L    -19 -11248 -12290   -894  -1115   -701  -1378  -7171  -6304
    65   -103  -4195    176   -803   -407    598  -3169    618   -250    684
-592    616   -392  -2836  -1348   -575    500    786  -4517   -956    65
     D   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     D    -19 -11169 -12211   -894  -1115   -701  -1378  -7171  -6285
    66  -3216    -41    863    117     14   1749   -370  -4753    -18   -877
1184    927  -1393   -238    899  -1126   -134  -1669  -4869  -1116    66
     G   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     G    -20 -11119 -12161   -894  -1115   -701  -1378  -7171  -6267
    67   -883    -66  -1410   -539  -4946   1730   1102  -1518   1448  -2272
-346   1076  -4239   -706    -71    146   -220   -811    543   -284    67
     R   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     R    -20 -11076 -12119   -894  -1115   -701  -1378  -7171  -6248
    68  -3135  -4561  -1467   -537   -307   -479  -2777    700   1697   -450  -
3655    168  -4209   -801   2141   -780    -67    349  -4756  -4085    68
     V   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     V    -20 -11004 -12046   -894  -1115   -701  -1378  -7171  -6229
    69   -554   1467  -1099    262  -1323  -4214  -2905   -212    965    313
-172  -1196    916   -979    443   -902    161   1207    401  -3800    69
     I   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     I    -20 -10946 -11988   -894  -1115   -701  -1378  -7171  -6209
    70   -286  -3937   -130    157   -851  -1526  -2879   1413    133   1121  -
3083  -2959    -59    -13    194  -3121  -1149    916  -4255    122    70
     D   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     D    -21 -10829 -11871   -894  -1115   -701  -1378  -7171  -6190
    71  -1515  -4363   -145   -970  -4677  -1647   -167    764   1490  -1304
 418   -973     10   -592   1727   -649   -596   1115  -4551   -717    71
     P   -149   -500    233     43   -381    399    106   -626    210   -466
-720    275    394     45     96    359    117   -369   -294   -249
     P    -21 -10478 -11520   -894  -1115   -701  -1378  -7171  -6170
    72  -1247   1262    534  -2707  -3242  -1113  -2669    654    698   -335  -
2371  -2868   -791   -448    781  -2905   -104   2274  -3578  -3123    72
     K      *      *      *      *      *      *      *      *      *      *
   *      *      *      *      *      *      *      *      *      *
     K      *      *      *      *      *      *      *  -7171      0
//

Output file format

   ehmmpfam outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: 7les_drome.ehmmpfam

Query:  7LES_DROME  SEVENLESS PROTEIN (EC 2.7.1.112).

Scores for sequence family classification (score includes all domains):
Model                Description                        Score    E-value  N
--------             -----------                        -----    ------- ---
7LES_DROME/2209-2481                                    115.9    7.6e-31   1
7LES_DROME/1799-1891                                     32.1    2.5e-06   1

Parsed for domains:
Model                Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------             ------- ----- -----    ----- -----      -----  -------
7LES_DROME/1799-1891   1/1    1799  1882 ..     1    84 []    32.1  2.5e-06
7LES_DROME/2209-2481   1/1    2209  2476 ..     1   268 []   115.9  7.6e-31

Alignments of top-scoring domains:
7LES_DROME/1799-1891: domain 1 of 1, from 1799 to 1882: score 32.1, E = 2.5e-06
7LES_DROME/2209-2481: domain 1 of 1, from 2209 to 2476: score 115.9, E = 7.6e-3
1
//

Data files

   **************** EDIT HERE ****************

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                Description
   ealistat      Statistics for multiple alignment files
   ehmmalign     Align sequences with an HMM
   ehmmbuild     Build HMM
   ehmmcalibrate Calibrate a hidden Markov model
   ehmmconvert   Convert between HMM formats
   ehmmemit      Extract HMM sequences
   ehmmfetch     Extract HMM from a database
   ehmmindex     Index an HMM database
   ehmmsearch    Search sequence database with an HMM

Author(s)

   This program is an EMBOSS conversion of a program written by Sean Eddy
   as part of his HMMER package.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
