                                  ehmmemit



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Generate sequences from a profile HMM

Description

   EMBASSY HMMER is a suite of application wrappers to the original hmmer
   v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be
   installed on the same system as EMBOSS and the location of the hmmer
   executables must be defined in your path for EMBASSY HMMER to work.

   Usage:
   ehmmemit [options] hmmfile outfile

   The outfile parameter is new to EMBASSY HMMER. The synthetic sequences
   are always written to outfile. The name of outfile is specified by the
   -o option as normal.

   hmmemit reads an HMM file from a file containing one or more HMMs, and
   generates a number of sequences from each HMM; or, if the -c option is
   selected, generate a single majority-rule consensus. This can be useful
   for various applications in which one needs a simulation of sequences
   consistent with a sequence family consensus. By default, hmmemit
   generates 10 sequences and outputs them in FASTA (unaligned) format
   file .

Algorithm

   Please read the Userguide.pdf distributed with the original HMMER and
   included in the EMBASSY HMMER distribution under the DOCS directory.

Usage

   Here is a sample session with ehmmemit


% ehmmemit ../ehmmcalibrate-ex-keep/globino.hmm globino.ehmmemit -c N -n 10
Generate sequences from a profile HMM.

hmmemit - generate sequences from a profile HMM
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:             ../ehmmcalibrate-ex-keep/globino.hmm
Number of seqs:       10
Random seed:          0
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Output saved in file globino.ehmmemit

/shared/software/bin/hmmemit --seed 0  -n 10  -o globino.ehmmemit ../ehmmcalibra
te-ex-keep/globino.hmm



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

Command line arguments

   Where possible, the same command-line qualifier names and parameter
   order is used as in the original hmmer. There are however several
   unavoidable differences and these are clearly documented in the "Notes"
   section below.

   More or less all options documented as "expert" in the original hmmer
   user guide are given in ACD as "advanced" options (-options must be
   specified on the command-line in order to be prompted for a value for
   them).

Generate sequences from a profile HMM.
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-hmmfile]           infile     File containing one or more HMMs.
   -c                  boolean    [N] Predict a single majority-rule consensus
                                  sequence instead of sampling sequences from
                                  the HMM's probability distribution. Highly
                                  conserved residues (p >= 0.9 for DNA, p >=
                                  0.5 for protein) are shown in upper case;
                                  others are shown in lower case. Some insert
                                  states may become part of the majority rule
                                  consensus, because they are used in >= 50%
                                  of generated sequences; when this happens,
                                  insert-generated residues are simply shown
                                  as 'x'.
*  -nseq               integer    [10] Generate  sequences. Default is 10.
                                  (Any integer value)
  [-o]                 outfile    [*.ehmmemit] File of synthetic sequences.

   Additional (Optional) qualifiers:
   -a                  boolean    [N] Write the generated sequences in an
                                  aligned format (SELEX) rather than FASTA.
   -q                  boolean    [N] Quiet; suppress all output except for
                                  the sequences themselves. Useful for piping
                                  or directing the output.

   Advanced (Unprompted) qualifiers:
   -seed               integer    [0] Set the random seed to , where  is
                                  a positive integer. The default is to use
                                  time() to generate a different seed for each
                                  run, which means that two different runs of
                                  hmmemit on the same HMM will give slightly
                                  different results. You can use this option
                                  to generate reproducible results. (Integer 0
                                  or more)

   Associated qualifiers:

   "-o" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


Input file format

  Alignment and sequence formats

   Input and output of alignments and sequences is limited to the formats
   that the original hmmer supports. These include stockholm, SELEX, MSF,
   Clustal, Phylip and A2M /aligned FASTA (alignments) and FASTA, GENBANK,
   EMBL, GCG, PIR (sequences). It would be fairly straightforward to adapt
   the code to support all EMBOSS-supported formats.

  Compressed input files

   Automatic processing of gzipped files is not supported.

   ehmmemit reads any normal sequence USAs.

  Input files for usage example

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

HMMER2.0  [2.3.2]
NAME  globins50
LENG  143
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850
000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.
hmm ../../data/hmmnew/globins50.msf
COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.00
0000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm
NSEQ  50
DATE  Thu Jan  7 16:51:40 2010
CKSUM 9858
XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -10
85   -142    -21   -313     45    531    201    384  -1998   -644
EVD   -35.959286   0.267496
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
         -450      *  -1900
     1    591  -1587    159   1351  -1874   -201    151  -1600    998  -1591   -
693    389  -1272    595     42    -31     27   -693  -1797  -1134    14
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378   -450      *
     2   -926  -2616   2221   2269  -2845  -1178   -325  -2678   -300  -2596  -1
810    220  -1592    939   -974   -671   -939  -2204  -2785  -1925    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     3   -638  -1715   -680    497  -2043  -1540     23  -1671   2380  -1641   -
840   -222  -1595    437   1040   -564   -523  -1363   2124  -1313    16
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     4    829  -1571    -37    660  -1856   -873    152  -1578    894  -1573   -
678    769  -1273   1284     58    224    447  -1175  -1782  -1125    17
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     5    369   -433   -475    286   -974  -1312    -19   -412    664    398
406   1030  -1394    388   -214   -261     85   -166  -1227   -725    18
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     6  -1291   -884  -3696  -3261  -1137  -3425  -2802   2322  -3066    111
 19  -3028  -3275  -2855  -3100  -2670  -1269   2738  -2450  -2062    19
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     7    157   -413   -236    316  -1387  -1231     89   -863   1084   -431   -
348    910  -1319    635    297     15    704   -483  -1497   -922    20
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     8    770  -1431    -43    459  -1751   -340     78  -1449    440  -1497   -
631    866  -1302    825    -51    953    364  -1076  -1750  -1121    21
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
     9    420   -186  -2172  -1577      8  -1818   -694   1477  -1281    760
614  -1299  -1867  -1001  -1262   -189    -12   1401   -722   -364    22
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
    10   -961   -879  -2277  -1821   1366  -2213   -204   -399  -1500   -130
-39  -1427  -2266  -1186  -1511   -159   -913   -367   4721   1177    23
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
    11    -48  -1782    809    844  -2073   1456      8  -1811    315  -1803   -
932    180  -1365    921   -218    173   -115  -1399  -2018  -1327    24


  [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
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   128   -415  -1926   1575   1399  -2219  -1163     17  -1983    527  -1929  -1
039    341  -1367   1597   -212    257   -222  -1536  -2109  -1387   144
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   129   -529  -1434   -629   -143  -1926   -626   -171  -1460   2679  -1597   -
839   -309  -1599    207    317   -530   -510   -130  -1840  -1369   145
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   130    811   -397  -2389  -1807   1883  -2039   -907    594  -1512   1077
687  -1532  -2065  -1201  -1483  -1125   -465   1067   -843   -472   146
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   131   -241   -102  -2327  -1710    724  -1767   -616    650  -1363   1074   1
765   -718  -1809  -1026  -1252   -842   -181   1331   -541    695   147
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   132    723     95    385    823  -1820  -1168    167  -1540    875  -1362   -
644    320  -1261    810    246    693    -67  -1141  -1753  -1098   148
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   133    551   -430  -1049   -481   -442    469   -241    465   -313    133
947   -411  -1543    197   -587   -146    202    522   -843   -429   149
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   134  -1086   -777  -3351  -2800    816  -2898  -1861   1501  -2515   1149
586  -2483  -2775  -2108  -2400  -2046  -1030   2380  -1511  -1216   150
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   135   1393   1409   -876   -345   -997   -525   -315   -590   -198   -847   -
109   -420  -1441    -97    412    766   -130    139  -1306   -858   151
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   136     98  -1299     36    365  -1495  -1211   1241   -404    523   -952   -
426   1174  -1303    511    -18    347    882   -853  -1566   -970   152
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   137   1308   -787    564   -132   -966  -1332   -203   -362    -49   -395
-57   -305  -1481     49   -437   -190   -182   1020  -1282   -802   153
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   138  -1746  -1358  -3897  -3341   -216  -3621  -2478   1774  -3040   2442   1
157  -3189  -3229  -2422  -2853  -2824  -1659    392  -1720  -1647   154
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   139   1176  -1289   -179    534  -1606   -607     34  -1278    734  -1372   -
534     44  -1325    433    -89    521    826   -941  -1666  -1072   155
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6528  -7571   -894  -1115   -701  -1378      *      *
   140    602  -1500   -135    850  -1753  -1214   1951  -1452    838  -1484
431    118  -1306    555    347    489   -153  -1085  -1723  -1092   156
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -22  -6602  -7644   -894  -1115   -701  -1378      *      *
   141    351  -1646   -165    546  -1976   -498     46  -1667   2193  -1662   -
798     35  -1405    476    311    -73   -306  -1287  -1859  -1254   157
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23  -6561  -7603   -894  -1115   -701  -1378      *      *
   142  -1995  -1606  -3095  -2870   1739  -3015    -98  -1012  -2520   -730
655  -1990  -2962  -1884  -2326  -2167  -1915  -1128    548   4089   158
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -25  -6455  -7497   -894  -1115   -701  -1378      *      *
   143   -253  -1373   -267    301   -911   -565   1956   -450   1188  -1330   -
497     33  -1352    502   1358   -205   -184   -941  -1604  -1026   159
     -      *      *      *      *      *      *      *      *      *      *
  *      *      *      *      *      *      *      *      *      *
     -      *      *      *      *      *      *      *      *      0
//

Output file format

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

  Output files for usage example

  File: globino.ehmmemit

>globins50-1
EESEKITERMGLMDGAHNKATETSLACLLKKLTPYPETKFSFAAYIRLKW
SEEPDLRKIALKVTDALTLTKIVQEIDDLMWKFQNGAVQHSRKQLNDIYF
KLIERILECSERRVGGATEAKLKKPITEIGKSQHRPVLGKGI
>globins50-2
AETSQVKIKWGKITEVCDEFPDAIFSSEWDLAELLHSQLMFMALTSVEAS
HEVRKSKTLKATGNQVLQVVVEAVPERDDMNGLLNELADTGCEEARISFY
FSILAKAIVNVLQPANEWIARIAYSAKAFIHTPGTVMNDSKR
>globins50-3
CDLDRCTLIYKQIDVRAEKVTGPARVFHSLADNHNAFPSCGDLTSRVTIL
RLPGIFNQADKVTGAIVNLTIKLNTDGIQVQSRDEQLHHAQYAVDIKSFT
EIIHCYLATVAPHKPDKYILEVFLVWQKRLTLTATDIGKQYG
>globins50-4
QWKNNVKRIFRQLQGNSRGHAHSALTFLLKKVPTTRDYLTQFKKFASGVE
WDEVCTNVMEEEKPGEMVARVQAGAEQRNELREVIREVSKIHAHEDYFDK
QRNSLLGQVVIERLLLHKGDNLEIQETESSSMQSAFISTWIKAGYQ
>globins50-5
KNRQKLDQISESITDDQAADGGQETITRVFGRRPSAKESFSEFLSSVRAF
EGQPEIRKGFMEVIYIFKEVVSPKGGLNATAAKLNVMLAYKLRVDPRFVV
LFLEAAEVLKCKQWDKVRFEFGSTIPEELRAIRRASGNYT
>globins50-6
GDKLTVLSYMREYKKYAPNSKESLAQMARAIPKTIAKKNYFKANHCMPVQ
ALTRIKTNGAKVLRYLNQIKNYGDMSGKLSNIGESHATSLSVGDENFPLN
SCIFVAGLDDVLDVSEDLTAEVHLGVDNLMQVVSHAVYLPKDLH
>globins50-7
DQEKVLFTQQKQGADRDNFGIIDCLNSPLDHMPWTRALVKMSRKSYEDKG
INQAEKQKLEGNSVLIVCVTALQSLDEVEQGISELLKHFACDLTIGKFQA
ICKGLPLRILLSGESSVMEPGAYASAQKRADVEAIVKEGKL
>globins50-8
DDKVNVKQVIQLIEKQLRTNGAEVLVHLLKVRPAREAAFQDWQRLHSGAA
FRDASVQTYGIEIVKSVGNAIEDTDNYMDRTIGKLSLMHARLRRIKPTGF
TLLKEVLTTINVLAVHNKAKFGPQSGRALSRIIKIVVNDLASDYK
>globins50-9
EDKAAANQGVSGVKKSKAKSTRPGLGRQFVKRPSAQEISRLFDLLDQTPT
SGDILRSADVDIQAHQCFPAFTNAYTIIDGMQGDWLKVLDAHWGFKGVHS
EATLYLAVIFVLPISLILQAELGTLKLYASERFYSRLIEVLGHKIT
>globins50-10
AEQAIEMQLWHAVANAKKVEEEQVKRLYQDERGSTAHFMHYEKLRNNNDK
VKQKGCTVLTVIKKQYKTLESDGSEVELLSSLEGDKDTLEIKLFVRLSDM
LITVLNNSTHNDESTHSEGASQAYFSGFSAVLAGKFT

Data files

   None.

Notes

  1. Command-line arguments

   The following original HMMER options are not supported:
-h         : Use -help to get help information instead.
-n         : Use -nseq instead (-n causes problems for GUI developers)

  2. Installing EMBASSY HMMER

   The EMBASSY HMMER package contains "wrapper" applications providing an
   EMBOSS-style interface to the applications in the original HMMER
   package version 2.3.2 developed by Sean Eddy. Please read the file
   INSTALL in the EMBASSY HMMER package distribution for installation
   instructions.

  3. Installing original HMMER

   To use EMBASSY HMMER, you will first need to download and install the
   original HMMER package. Please read the file 00README in the the
   original HMMER package distribution for installation instructions:
WWW home:       http://hmmer.wustl.edu/
Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/

  4. Setting up HMMER

   For the EMBASSY HMMER package to work, the directory containing the
   original HMMER executables *must* be in your path. For example if you
   executables were installed to "/usr/local/hmmer/bin", then type:
set path=(/usr/local/hmmer/bin/ $path)
rehash

  5. Getting help

   Please read the Userguide.pdf distributed with the original HMMER and
   included in the EMBASSY HMMER distribution under the DOCS directory.
   The first 3 chapters (Introduction, Installation and Tutorial) are
   particularly useful.

   Please read the 'Notes' section below for a description of the
   differences between the original and EMBASSY HMMER, particularly which
   application command line options are supported.

References

   None.

Warnings

  Types of input data

   hmmer v3.2.1 and therefore EMBASSY HMMER is only recommended for use
   with protein sequences. If you provide a non-protein sequence you will
   be reprompted for a protein sequence. To accept nucleic acid sequences
   you must replace instances of < type: "protein" > in the application
   ACD files with .

  Environment variables

   The original hmmer uses BLAST environment variables (below), if
   defined, to locate files. The EMBASSY HMMER does not.
BLASTDB   location of sequence databases to be searched
BLASMAT   location of substitution matrices
HMMERDB   location of HMMs

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                    Program name                      Description
                    ehmmalign     Align sequences to an HMM profile
                    ehmmbuild     Build a profile HMM from an alignment
   ehmmcalibrate    Calibrate HMM search statistics
                    ehmmconvert   Convert between profile HMM file formats
                    ehmmfetch     Retrieve an HMM from an HMM database
                    ehmmindex     Create a binary SSI index for an HMM database
                    ehmmpfam      Search one or more sequences against an HMM database
                    ehmmsearch    Search a sequence database with a profile HMM
                    oalistat      Statistics for multiple alignment files
                    ohmmalign     Align sequences with an HMM
                    ohmmbuild     Build HMM
   ohmmcalibrate    Calibrate a hidden Markov model
                    ohmmconvert   Convert between HMM formats
                    ohmmemit      Extract HMM sequences
                    ohmmfetch     Extract HMM from a database
                    ohmmindex     Index an HMM database
                    ohmmpfam      Align single sequence with an HMM
                    ohmmsearch    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. Jon Ison (jison (c) ebi.ac.uk)
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    This program is an EMBASSY wrapper to a program written by Sean Eddy as
                    part of his hmmer package.

                    Please report any bugs to the EMBOSS bug team in the first instance,
                    not to Sean Eddy.

History

Target users

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