                                  ehmmindex



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Create a binary SSI index for an HMM database

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:
   ehmmindex [options] database

   hmmindex is a utility that creates a binary SSI ('squid sequence index'
   format) index for an HMM database file called . The new index file is
   named database.ssi. An SSI index file is required for hmmfetch to work,
   and also for the PVM implementation of hmmpfam.

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 ehmmindex


% ehmmindex myhmmso
Create a binary SSI index for an HMM database.

hmmindex -- create SSI index for an HMM database
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:                 ./myhmmso
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Determining offsets for ./myhmmso, please be patient...
Complete.
HMM file:       ./myhmmso
SSI index:      ./myhmmso.ssi
# of HMMS:      3
HMM names:      3
HMM accessions: 2

/shared/software/bin/hmmindex ./myhmmso



   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).

Create a binary SSI index for an HMM database.
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-database]          infile     HMM database.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   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.

   ehmmindex reads any normal sequence USAs.

Output file format

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

  Output files for usage example

  File: myhmmso.ssi

   This file contains non-printing characters and so cannot be displayed
   here.

  File: myhmmso

HMMER2.0  [2.3.2]
NAME  rrm
LENG  77
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /shared/software/bin/hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --
idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../
data/hmmnew/rrm.sto
COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.00
0000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ  90
DATE  Thu Jan  7 16:51:40 2010
CKSUM 8325
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   -45.860321   0.213107
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
          -16      *  -6492
     1  -1084    390  -8597  -8255  -5793  -8424  -8268   2395  -8202   2081  -1
197  -8080  -8115  -8020  -8297  -7789  -5911   1827  -7525  -7140     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378    -16      *
     2  -2140  -3785  -6293  -2251   3226  -2495   -727   -638  -2421   -545   -
675  -5146  -5554  -4879  -1183  -2536  -1928    267     76   3171     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     3  -2542    458  -8584  -8273  -6055  -8452  -8531   2304  -8255   -324
101  -8104  -8170  -8221  -8440  -7840  -5878   3145  -7857  -7333     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     4  -1505  -5144  -1922   -558  -1842   2472  -3303  -2213   1099  -5160  -4
233    372  -4738   -530   1147    168    498  -4766  -5327  -1476     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     5  -3724  -5184    300  -3013  -1655   1803  -3353  -5245  -1569  -2686  -4
276   3495  -1963  -1331  -1054  -1472  -3664  -4803  -5369     -2     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     6  -1569  -6106  -8967  -8363    555  -8531  -7279    654  -8092   2953
-94  -8220  -7908  -1643  -7682  -7771  -6460    -59  -6191  -6284     6
     -   -151   -504    230     45   -380    399    101   -621    211   -470   -
713    278    399     48     91    360    113   -364   -299   -254
     -   -178  -3113 -12684  -1600   -578   -701  -1378      *      *
     7   -409  -5130   -215  -2987  -1709   -956    690  -5188   -395  -5144  -4
224    729   3054  -2862  -3409    354   1293  -1381  -5321  -4644    13
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     8  -3674  -5118  -1004    639    420  -4652    176  -2050    404  -1039   -
935     16   1755    168    147   -275    198  -1472   1889   1977    14
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     9   -408  -5134   2415   1299   -950    -66   -767  -1296  -2889  -1843  -4
224   1084   -968  -1439  -1854    540   -314  -2304  -5320    -60    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
    10    586   1804  -6294   -631  -1627  -1671  -4374   1029  -2223   -162   1
172  -5147  -5554  -1870  -5058  -2327   1741   1687  -4242    687    16
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
    11  -2134  -5144    845  -1187  -1652  -1667  -3303  -5216   -513   -801  -4
233   1026  -1873   -543   -619    575   2956  -4766  -5327  -4644    17


  [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
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   279  -7207  -7306  -8076  -6588  -8459  -7223  -5448  -7982  -1500  -7531  -6
953  -6369  -7277  -5081   4236  -7139  -6862  -7777  -7053  -7277   454
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   280   -694   -163  -5922  -5286  -1204  -2048   -610   1082  -1800   1434  -2
618  -4776   2951  -4509  -4688  -1216  -1648  -2829    202     21   455
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -  -3168 -11253   -171   -894  -1115   -701  -1378      *      *
   281  -1412  -2132  -2007  -2293  -4366   3113  -2847  -4225  -3107  -4377  -3
503   1660  -2881  -2661  -3396    961  -1821  -3134  -4516  -4119   456
     -   -150   -489    232     42   -382    400    104   -627    211   -465   -
722    274    393     51     95    359    116   -370   -296   -245
     -  -2121   -637  -2975   -831  -1191  -6099    -21      *      *
   282   -968  -1818  -1787  -1351  -3112    953  -1494  -2818  -1122  -2911  -2
044  -1365  -2340  -1133   1510   1816   2121  -2205  -3137  -2649   459
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -   -228  -7899  -2816   -894  -1115  -4964    -47      *      *
   283    840  -1663   -994    969   1159    503   -604  -1413   -325  -1594   -
814   -688  -1996   -267   1103   -851   -755  -1179   2900  -1437   460
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -9  -7938  -8980   -894  -1115    -89  -4060      *      *
   284  -3257  -4642   -697  -2590  -1218   -252  -2907  -4655  -1306  -2353   -
529    482  -1607  -2459  -1398   2112   2745  -4246  -4848  -4187   461
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11183 -12226   -894  -1115   -186  -3045      *      *
   285   2163    763  -1619  -5296   2250  -2060  -4007   1241  -4891   -489
484  -4781   -226  -4515  -4692   -678  -1688   -813    264  -3530   462
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   286   -268   -329   -158    917   -541  -1990    350  -4851   1273  -1075
388  -1130    233    840    993   -602    801   -595  -4964   -857   463
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   287    109   -243    672   2304  -5103  -4283    488  -4854  -1317  -2269   -
656   -492  -1519   2679   -655   -618  -3248  -4404  -4965  -1114   464
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   288   1312   1294  -6215  -5593   -206  -1244  -4339   2188  -5201   1409
395  -5091  -5478  -4828  -5009  -4538  -3794   1162  -4187  -3846   465
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23 -11253  -6022   -894  -1115   -701  -1378      *      *
   289  -3562    799  -5767  -2054  -1235  -2075    318    138    237   2164   1
713  -1454  -5145  -1272   -730  -4172  -1640   1071  -3865    -34   466
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11231 -12273   -894  -1115  -1470   -646      *      *
   290     73   1351   -674   1236  -1549  -2008   1350  -4834   1049  -2498  -3
851   1801  -4356   1813   -115   -223  -1582  -1052  -4945  -4262   467
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      *
   291  -1739   -320    777  -2654  -1419  -2051   4360  -4707  -1358  -2412   -
689  -1300  -4399   -224    537    531   -289  -2010  -4905  -1057   468
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   292  -3345  -4494   -233   -332   -563  -1986  -3051    333     99   1063  -3
616  -3072   2953  -1026  -1490   -943  -1528  -1070  -4753  -4151   469
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -10815 -11857   -894  -1115   -701  -1378      *      *
   293  -6409  -5751  -7614  -7636   2593  -7311  -4003  -5084  -7219   -150   -
151  -6210  -7172   -849  -6723  -6510  -6299  -1387   4881   2807   470
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -10749 -11791   -894  -1115   -701  -1378      *      *
   294  -4057  -3817  -6415  -5791   3203  -1638  -4541   1679  -5412    765   1
434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
     -      *      *      *      *      *      *      *      *      *      *
  *      *      *      *      *      *      *      *      *      *
     -      *      *      *      *      *      *      *      *      0
//

Data files

   None.

Notes

  1. Command-line arguments

   The following original HMMER options are not supported:
-h         : Use -help to get help information instead.

  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

  Output file

   The index file is hardcoded to database.ssi (where database is the name
   of the database that was indexed) and is written to the same directory
   as the input file. This behaviour could be changed in the future.

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
                    ehmmemit      Generate sequences from a profile HMM
                    ehmmfetch     Retrieve an HMM from 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.
