ehmmsearch

 

Function

Search sequence database with an HMM

Description

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

Algorithm

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

Usage

Here is a sample session with ehmmsearch


% ehmmsearch Artemia.fa ../ehmmcalibrate-ex-keep/globin.hmm -auto 

                   *->vlstaeeklvkaswgkkvnvaeeggeellrrlfvsppttktffsh<-
                      +ls  e+ ++++ wgk+ ++ +e+g + +  lf  +p+   +f +  
      S13421   303    GLSGLEKNAILSTWGKVRGNLQEVGKATFGKLFTAHPEYQQMFRF   347  

                   *
                    
      S13421     -   -    

score    obs    exp  (one = represents 1 sequences)
-----    ---    ---
   12      1      0|=                                                          


% Statistical details of theoretical EVD fit:
              mu =    -7.9790
          lambda =     0.6465
chi-sq statistic =     0.0000
  P(chi-square)  =          0
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         19K
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         19K

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:
   -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>.ehmmsearch
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-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

ehmmsearch reads any normal sequence USAs.

Input files for usage example

File: Artemia.fa

>S13421 S13421 GLOBIN - BRINE SHRIMP
DKATIKRTWATVTDLPSFGRNVFLSVFAAK
PEYKNLFVEFRNIPASELASSERLLYHGGR
VLSSIDEAIAGIDTPDRAVKTLLALGERHI
SRGTVRRHFEAFSYAFIDELKQRGVESADL
AAWRRGWDNIVNVLEAGLLRRQIDLEVTGL
SCVDVANIQESWSKVSGDLKTTGSVVFQRM
INGHPEYQQLFRQFRDVDLDKLGESNSFVA
HVFRVVAAFDGIIHELDNNQFIVSTLKKLG
EQHIARGTDISHFQNFRVTLLEYLKENGMN
GAQKASWNKAFDAFEKYISMGLSSLKRVDP
ITGLSGLEKNAILSTWGKVRGNLQEVGKAT
FGKLFTAHPEYQQMFRFSQGMPLASLVESP
KFAAHTQRVVSALDQTLLALNRPSDFVYMI
KELGLDHINRGTDRSHFENYQVVFIEYLKE
TLGDSLDEFTVKSFNHVFEVIISFLNEGLR
QADIVDPVTHLTGRQKEMIKASWSKARTDL
RSLGQELFMRMFKAHPEYQTLFVNKGFADV
PLVSLREDERFISHMANVLGGFDTLLQNLD
ESSYFIYSLRNLGDAHIQRKAGTQHFRSFE
AILIPILQESQGLDAASVEAWKKFFDVSIG
VIAQGLKVATSEEADPVTGLYGKEIVALRQ
AFAAVTPRNVEIGKRVFAKLFAAHPEYKNL
FKKFEQYSVEELPSTDAFHYHISLVMNRFS
SIGKVIDDNVSFVYLLKKLGREHIKRGLSR
KQFDQFVELYIAEISSELSDTGRNGLEKVL
TFATGVIEQGLFQLGQVDSNTLTALEKQSI
QDIWSNLRSTGLQDLAVKIFTRLFSAHPEY
KLLFTGRFGNVDNINENAPFKAHLHRVLSA
FDIVISTLDDSEHLIRQLKDLGLFHTRLGM
TRSHFDNFATAFLSVAQDIAPNQLTVLGRE
SLNKGFKLMHGVIEEGLLQLERINPITGLS
AREVAVVKQTWNLVKPDLMGVGMRIFKSLF
EAFPAYQAVFPKFSDVPLDKLEDTPAVGKH
SISVTTKLDELIQTLDEPANLALLARQLGE
DHIVLRVNKPMFKSFGKVLVRLLENDLGQR
FSSFASRSWHKAYDVIVEYIEEGLQQSYKQ
DPVTGITDAEKALVQESWDLLKPDLLGLGR
KIFTKVFTKHPDYQILFTRTGFGDTPLTKL
DDNPAFGTHIIKVMRAFDHVIQILGKPKTL
MAYLRSVGADHIATNVERRHFQAFSNALIP
VMQHDLKAQLRPDAVAAWRKGLDRIIGIID
QGLIGLKEVNPQNAFSAYDIQAVQRTWALA
KPDLMGKGAMVFKQLFTDHGYQPLFSNLAQ
YEITGLEGSPELNTHARNVMAQLDTLVGSL
QNSIELGQSLAQLGKDHVPRKVNRVHFKDF
AEHFIPLMKADLGDEFTPLAESAWKRAFDV
MIATIEQGQEGSSHALSSFLTNPVA

File: ../ehmmcalibrate-ex-keep/globin.hmm

HMMER2.0
NAME  globins50
LENG  146
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   ehmmbuild ../../data/hmm/globins50.msf globin.hmm -auto
COM   ehmmcalibrate globin.hmm -seed 1079460101 -auto
NSEQ  50
DATE  Fri Feb 18 10:17:03 2005
CKSUM 5854
XT      -8455     -4      0      *  -8455     -4      0      * 
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
EVD    -7.978981   0.646464
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
          -93      *  -4000
     1  -1967  -2271  -4498  -4217  -3055   1639  -3307  -2518  -3920  -2945   2068  -3352    193  -3569  -3796    257  -2222   2801  -3514  -3205     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -1093  -8180 
     2  -1670  -1776    -76  -2279   1025  -3037   3194    232    -52   1914   -955  -2245  -3102  -1004  -2223  -2065  -1610  -1207  -2178  -1775     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8175 
     3  -1713  -1550  -3992  -3365    801  -3249  -2111  -1027  -2974    762   -736  -2876  -3301  -2606  -2796   1725   1747    269   3309  -1618     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8170 
     4   1140  -2941   1606    792  -3253  -2463  -1127   -278    -63  -2954  -2034  -1102   -473   -671  -1220    572   1661  -2558  -3131  -2454     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8165 
     5   1794  -2944    -65   -235  -3261    829  -1114   -284   1649  -2958  -2034   -134  -1104   -656  -1204     60   -589  -2564  -3130  -2449     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8160 
     6  -1748  -3220   1958   2253  -3519    172  -1355  -3271   -993   -829  -2323  -1243  -2761   1731  -1518  -1165  -1696   -335  -3410  -2713     6
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8155 
     7   -173  -2945   -205   2098  -3264  -2452  -1111   -302   1817  -2960  -2035    433  -2545   -652   -261    -62  -1417  -2566   2430  -2449     7
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8150 
     8    933  -2910  -1344   -795  -3214  -1181  -1120  -2952   2227   -837  -2004   -157  -2553   1184   -129    241    381   -316  -3104  -2432     8
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8145 
     9   1054   1483  -2717  -2142  -1752  -2967  -1753   -661   -506    965    533   1919  -3033    494  -2159    300   -763    120  -2182  -1788     9
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8140 
    10    475   -184  -3984   -927  -1458  -3217  -2087    964  -2953    185   -705  -2852     14  -2583  -2766  -2300   -535   2595   1896  -1619    10
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -     -9  -9065 -10107   -894  -1115   -701  -1378  -8273  -8134 
    11   -171  -2034  -2133  -1572  -2075  -2788  -1524   1191   1414    546  -1206    859  -2865    894  -1789    -14   -603   1034  -2415  -1962    11


  [Part of this file has been deleted for brevity]

     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7331 
   131   1046  -2920    936    659  -3228  -2456  -1116  -1039    363  -2931   1609   -673  -2549   2249  -1206   -311   -848    236  -3111  -2436   131
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7322 
   132   1525  -2380  -1743  -1189  -2505  -2643  -1343    -80   2077  -2311  -1534   -729  -2731    501  -1500   -603   -889   1459  -2705  -2176   132
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7313 
   133    738  -1513  -3848  -3222   -198    361  -2054    325    428   1007   -714  -2784  -3243  -2505  -2708    324  -1602   1238  -1968   1351   133
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7304 
   134    987   1437    598    -22    375   -425  -1546   -562  -1482  -1887    629    128  -2881  -1372  -1826   -262    958   1290  -2386  -1941   134
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7295 
   135   1231  -2587  -1541    216  -2769    193  -1233  -2428    -54    355  -1715   -467  -2642   -839   -418    386  -1448   1716  -2861  -2275   135
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7285 
   136    606  -2680    165    660  -2889    865  -1213  -2564    326   1588  -1802  -1227  -2627   -803  -1338  -1459   -507     11  -2936  -2329   136
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7276 
   137    804  -1523  -4031  -3398  -1482  -3248  -2124    348  -2998   1327   -725  -2891  -3297  -2625  -2804  -1588   1321   1922   1901  -1649   137
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7267 
   138   1808  -1941  -2321    901    973   -408  -1613  -1543  -1607  -1831   1197  -1869  -2928  -1483  -1921    869    632     -3  -2347  -1916   138
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7257 
   139   1340  -2950   -394    203  -3271  -2451   1896  -1633   1977  -2966  -2040   1016  -2545   -650    779    -62  -1417  -2572  -3134  -2451   139
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -13  -9069 -10111   -894  -1115   -701  -1378  -8273  -7248 
   140   1476  -2348  -1739    120  -2460  -2637  -1336    497    345  -2272   1946    710  -2722  -1006  -1512   -916    102  -1854  -2672   2397   140
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -14  -9069 -10111   -894  -1115   -701  -1378  -8273  -7238 
   141  -1642  -1910    588  -1926    393  -2933  -1677    165   1129   1319  -1086  -1997  -3002  -1605   1807  -1932  -1580  -1356  -2286   1485   141
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -15  -8608  -9650   -894  -1115   -701  -1378  -8273  -7229 
   142   1542   1691    488   -582  -2626   -279   -862    506   1171  -2375   -136   -872  -2282   -440    468    312  -1114  -1970  -2642  -2022   142
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8505  -9547   -894  -1115   -701  -1378  -8273  -7219 
   143   2278  -2091  -2495  -1900  -2272  -2771   3583    522  -1069  -2122  -1438  -1912  -2941  -1387    524  -1886  -1664  -1689  -2531  -2110   143
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8405  -9447   -894  -1115   -701  -1378  -8273  -7209 
   144   1313  -1624  -1590  -1030    784    176  -1023  -1263   1746    -28   1368  -1204  -2374   -799   -322   -323  -1039  -1096  -1996  -1532   144
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -8405  -9447   -894  -1115   -701  -1378  -8273  -7200 
   145  -2395  -2460  -3209  -2720   1335  -3543  -1417  -2096   1716     53  -1668    854  -3574  -2202  -2474  -2599  -2321  -2018  -1148   3600   145
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -17  -8323  -9365   -894  -1115   -701  -1378  -8273  -7190 
   146  -1328  -1570  -2202  -1667   1530    183   3522  -1184  -1501  -1451   -788  -1688  -2680  -1341  -1757    347    444  -1057  -1556   1992   146
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *  -8273      0 
//

Output file format

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

Output files for usage example

File: s13421.ehmmsearch


Query HMM: globins50||
  [HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
S13421   GLOBIN - BRINE SHRIMP                           12.7      0.089   1

Parsed for domains:
Sequence Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
S13421     1/1     303   347 ..     1    45 [.    12.7    0.089

Alignments of top-scoring domains:
S13421: domain 1 of 1, from 303 to 347: score 12.7, E = 0.089

Histogram of all scores:

Total sequences searched: 1

Whole sequence top hits:

Domain top hits:

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 nameDescription
ealistatStatistics for multiple alignment files
ehmmalignAlign sequences with an HMM
ehmmbuildBuild HMM
ehmmcalibrateCalibrate a hidden Markov model
ehmmconvertConvert between HMM formats
ehmmemitExtract HMM sequences
ehmmfetchExtract HMM from a database
ehmmindexIndex an HMM database
ehmmpfamAlign single sequence 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.