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Function
Build a profile HMM from an alignmentDescription
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:
ehmmbuild [options] alignfile hmmfile
Important note: the alignfile (input) and hmmfile (output) parameters are specified in the reverse order in the original HMMER.
hmmbuild reads a multiple sequence alignment file
Go to the input files for this example
Example 2
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Example 3
Go to the input files for this example
Example 4
Go to the input files for this example
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).
ehmmbuild reads any normal sequence USAs.
The following additional options are provided:
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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Jon Ison
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
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.
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 ehmmbuild
% ehmmbuild globins50.msf globin.hmm -nhmm globins50 -strategy D
Build a profile HMM from an alignment.
hmmbuild - build a hidden Markov model from an alignment
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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file: ../../data/hmmnew/globins50.msf
File format: MSF
Search algorithm configuration: Multiple domain (hmmls)
Model construction strategy: MAP (gapmax hint: 0.50)
Null model used: (default)
Prior used: (default)
Sequence weighting method: G/S/C tree weights
New HMM file: globin.hmm [appending]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment: #1
Number of sequences: 50
Number of columns: 308
Determining effective sequence number ... done. [2]
Weighting sequences heuristically ... done.
Constructing model architecture ... done.
Converting counts to probabilities ... done.
Setting model name, etc. ... done. [globins50]
Constructed a profile HMM (length 143)
Average score: 189.04 bits
Minimum score: -17.62 bits
Maximum score: 234.09 bits
Std. deviation: 53.18 bits
Finalizing model configuration ... done.
Saving model to file ... done.
//
/shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf
Go to the output files for this example
% ehmmbuild rrm.sto myhmms -nhmm rrm -strategy D
Build a profile HMM from an alignment.
hmmbuild - build a hidden Markov model from an alignment
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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file: ../../data/hmmnew/rrm.sto
File format: Stockholm
Search algorithm configuration: Multiple domain (hmmls)
Model construction strategy: MAP (gapmax hint: 0.50)
Null model used: (default)
Prior used: (default)
Sequence weighting method: G/S/C tree weights
New HMM file: myhmms [appending]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment: #1
Number of sequences: 90
Number of columns: 104
Determining effective sequence number ... done. [88]
Weighting sequences heuristically ... done.
Constructing model architecture ... done.
Converting counts to probabilities ... done.
Setting model name, etc. ... done. [rrm]
Constructed a profile HMM (length 77)
Average score: 75.37 bits
Minimum score: 26.86 bits
Maximum score: 119.83 bits
Std. deviation: 21.78 bits
Finalizing model configuration ... done.
Saving model to file ... done.
//
/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
Go to the output files for this example
% ehmmbuild fn3.sto myhmms -nhmm fn3 -strategy D
Build a profile HMM from an alignment.
hmmbuild - build a hidden Markov model from an alignment
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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file: ../../data/hmmnew/fn3.sto
File format: Stockholm
Search algorithm configuration: Multiple domain (hmmls)
Model construction strategy: MAP (gapmax hint: 0.50)
Null model used: (default)
Prior used: (default)
Sequence weighting method: G/S/C tree weights
New HMM file: myhmms [appending]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment: fn3
Number of sequences: 108
Number of columns: 119
Determining effective sequence number ... done. [108]
Weighting sequences heuristically ... done.
Constructing model architecture ... done.
Converting counts to probabilities ... done.
Setting model name, etc. ... done. [fn3]
Constructed a profile HMM (length 84)
Average score: 67.54 bits
Minimum score: 27.53 bits
Maximum score: 105.77 bits
Std. deviation: 17.07 bits
Finalizing model configuration ... done.
Saving model to file ... done.
//
/shared/software/bin/hmmbuild -n fn3 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/fn3.sto
Go to the output files for this example
% ehmmbuild pkinase.sto myhmms -nhmm pkinase -strategy D
Build a profile HMM from an alignment.
hmmbuild - build a hidden Markov model from an alignment
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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment file: ../../data/hmmnew/pkinase.sto
File format: Stockholm
Search algorithm configuration: Multiple domain (hmmls)
Model construction strategy: MAP (gapmax hint: 0.50)
Null model used: (default)
Prior used: (default)
Sequence weighting method: G/S/C tree weights
New HMM file: myhmms [appending]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Alignment: pkinase
Number of sequences: 67
Number of columns: 471
Determining effective sequence number ... done. [67]
Weighting sequences heuristically ... done.
Constructing model architecture ... done.
Converting counts to probabilities ... done.
Setting model name, etc. ... done. [pkinase]
Constructed a profile HMM (length 294)
Average score: 312.79 bits
Minimum score: 176.48 bits
Maximum score: 390.44 bits
Std. deviation: 44.60 bits
Finalizing model configuration ... done.
Saving model to file ... done.
//
/shared/software/bin/hmmbuild -n pkinase --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/pkinase.sto
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.
Build a profile HMM from an alignment.
Version: EMBOSS:6.3.0
Standard (Mandatory) qualifiers:
[-alignfile] seqset (Aligned) protein sequence set filename and
optional format, or reference (input USA)
-nhmm string Name for this HMM. The name can be any
string of non-whitespace characters (e.g.
one 'word'). There is no length limit (at
least not one imposed by HMMER; your shell
will complain about command line lengths
frst). (Any word)
-strategy menu [D] All alignments are local with respect to
the sequence and are configured to be local
(fragmentary) or global with respect to the
HMM. The model is also configured to find a
single or multiple domains (matches) to a
sequence. The options for configuring the
model are as follows: (D): The default
setting. Multiple domains per sequence,
global alignments with respect to the HMM.
(F): Multiple domains per sequence, local
alignments with respect to the HMM.
Analogous to the old hmmfs program of HMMER
1. (G) Single domain per sequence, global
alignment with respect to the HMM. Analogous
to the old hmms program of HMMER 1. (S)
Single domain per sequence, local alignments
with respect to the HMM. Analogous to the
old hmmsw program of HMMER 1. (Values: D
(global-multidomain); F (local-multidomain);
G (global-singledomain); S
(local-singledomain))
[-hmmfile] outfile [*.ehmmbuild] HMMER hidden markov model
output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-prior infile Read a Dirichlet prior from file, replacing
the default mixture Dirichlet. The format of
prior files is documented in the User's
Guide, and an example is given in the Demos
directory of the HMMER distribution.
-null infile Read a null model from file. The default for
protein is to use average amino acid
frequencies from Swissprot 34 and p1 =
350/351; for nucleic acid, the default is to
use 0.25 for each base and p1 = 1000/1001.
For documentation of the format of the null
model file and further explanation of how
the null model is used, see the User's
Guide.
-pam infile Apply a heuristic PAM- (substitution
matrix-) based prior on match emission
probabilities instead of the default mixture
Dirichlet. The substitution matrix is read
from file. See -pamwgt. The default
Dirichlet state transition prior and insert
emission prior are unaffected. Therefore in
principle you could combine -prior with -pam
but this isn't recommended, as it hasn't
been tested. ( -pam itself hasn't been
tested much!)
-pamwgt float [20.0] Controls the weight
Qualifier
Type
Description
Allowed values
Default
Standard (Mandatory) qualifiers
[-alignfile]
(Parameter 1)seqset
(Aligned) protein sequence set filename and optional format, or reference (input USA)
Readable set of sequences
Required
-nhmm
string
Name for this HMM. The name can be any string of non-whitespace characters (e.g. one 'word'). There is no length limit (at least not one imposed by HMMER; your shell will complain about command line lengths frst).
Any word
-strategy
list
All alignments are local with respect to the sequence and are configured to be local (fragmentary) or global with respect to the HMM. The model is also configured to find a single or multiple domains (matches) to a sequence. The options for configuring the model are as follows: (D): The default setting. Multiple domains per sequence, global alignments with respect to the HMM. (F): Multiple domains per sequence, local alignments with respect to the HMM. Analogous to the old hmmfs program of HMMER 1. (G) Single domain per sequence, global alignment with respect to the HMM. Analogous to the old hmms program of HMMER 1. (S) Single domain per sequence, local alignments with respect to the HMM. Analogous to the old hmmsw program of HMMER 1.
D (global-multidomain) F (local-multidomain) G (global-singledomain) S (local-singledomain) D
[-hmmfile]
(Parameter 2)outfile
HMMER hidden markov model output file
Output file
<*>.ehmmbuild
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-prior
infile
Read a Dirichlet prior from file, replacing the default mixture Dirichlet. The format of prior files is documented in the User's Guide, and an example is given in the Demos directory of the HMMER distribution.
Input file
Required
-null
infile
Read a null model from file. The default for protein is to use average amino acid frequencies from Swissprot 34 and p1 = 350/351; for nucleic acid, the default is to use 0.25 for each base and p1 = 1000/1001. For documentation of the format of the null model file and further explanation of how the null model is used, see the User's Guide.
Input file
Required
-pam
infile
Apply a heuristic PAM- (substitution matrix-) based prior on match emission probabilities instead of the default mixture Dirichlet. The substitution matrix is read from file. See -pamwgt. The default Dirichlet state transition prior and insert emission prior are unaffected. Therefore in principle you could combine -prior with -pam but this isn't recommended, as it hasn't been tested. ( -pam itself hasn't been tested much!)
Input file
Required
-pamwgt
float
Controls the weight <x> on a PAM-based prior. Only has effect if -pam option is also in use. <x> is a positive real number, 20.0 by default. <x> is the number of 'pseudocounts' contriubuted by the heuristic prior. Very high values of <x> can force a scoring system that is entirely driven by the substitution matrix, making HMMER somewhat approximate Gribskov profiles.
Any numeric value
20.0
-pbswitch
integer
For alignments with a very large number of sequences, the GSC, BLOSUM, and Voronoi weighting schemes are slow; they're O(N^2) for N sequences. Henikoff position-based weights (PB weights) are more effcient. At or above a certain threshold sequence number <n> hmmbuild will switch from GSC, BLOSUM, or Voronoi weights to PB weights. To disable this switching behavior (at the cost of compute time, set <n> to be something larger than the number of sequences in your alignment. <n> is a positive integer; the default is 1000.
Any integer value
1000
-archpri
float
The value of the 'architecture prior' used by MAP architecture construction. This value is a probability between 0 and 1. This parameter governs a geometric prior distribution over model lengths. As 'archpri' increases, longer models are favored a priori. As 'archpri' decreases, it takes more residue conservation in a column to make a column a 'consensus' match column in the model architecture. The 0.85 default has been chosen empirically as a reasonable setting.
Any numeric value
0.85
-binary
boolean
Write the HMM to file in HMMER binary format instead of readable ASCII text.
Boolean value Yes/No
No
-fast
boolean
Quickly and heuristically determine the architecture of the model by assigning all columns with more than a certain fraction of gap characters to insert states. By default this fraction is 0.5, and it can be changed using the --gapmax option. The default construction algorithm is a maximum a posteriori (MAP) algorithm, which is slower.
Boolean value Yes/No
No
-gapmax
float
Controls the -fast model construction algorithm, but if -fast is not being used, has no effect. If a column has more than a fraction <x> of gap symbols in it, it gets assigned to an insert column. <x> is a frequency from 0 to 1, and by default is set to 0.5. Higher values of <x> mean more columns get assigned to consensus, and models get longer; smaller values of <x> mean fewer columns get assigned to consensus, and models get smaller.
Any numeric value
0.5
-hand
boolean
Specify the architecture of the model by hand: the alignment file must be in SELEX or Stockholm format, and the reference annotation line (RF in SELEX, GC RF in Stockholm) is used to specify the architecture. Any column marked with a non-gap symbol (such as an 'x', for instance) is assigned as a consensus (match) column in the model.
Boolean value Yes/No
No
-sidlevel
float
Controls both the determination of effective sequence number and the behavior of the -wblosum weighting option. The sequence alignment is clustered by percent identity, and the number of clusters at a cutoff threshold of <x> is used to determine the effective sequence number. Higher values of <x> give more clusters and higher effective sequence numbers; lower values of <x> give fewer clusters and lower effective sequence numbers. <x> is a fraction from 0 to 1, and by default is set to 0.62 (corresponding to the clustering level used in constructing the BLOSUM62 substitution matrix).
Any numeric value
0.62
-noeff
boolean
Turn off the effective sequence number calculation, and use the true number of sequences instead. This will usually reduce the sensitivity of the final model (so don't do it without good reason!)
Boolean value Yes/No
No
-swentry
float
Controls the total probability that is distributed to local entries into the model, versus starting at the beginning of the model as in a global alignment. <x> is a probability from 0 to 1, and by default is set to 0.5. Higher values of <x> mean that hits that are fragments on their left (N or 5'-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of <x> mean that fragments on the left will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5'/3') termini of your target sequences using --swentry and --swexit.
Any numeric value
0.5
-swexit
float
Controls the total probability that is distributed to local exits from the model, versus ending an alignment at the end of the model as in a global alignment. <x> is a probability from 0 to 1, and by default is set to 0.5. Higher values of <x> mean that hits that are fragments on their right (C or 3'-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of <x> mean that fragments on the right will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5'/3') termini of your target sequences using -swentry and -swexit.
Any numeric value
0.5
-verbosity
boolean
Print more possibly useful stuff, such as the individual scores for each sequence in the alignment.
Boolean value Yes/No
No
-weighting
list
Values (B)(-wblosum in HMMER) Use the BLOSUM filtering algorithm to weight the sequences. Cluster the sequences at a given percentage identity (see -idlevel); assign each cluster a total weight of 1.0, distributed equally amongst the members of that cluster. (G)(-wgsc in HMMER) Use the Gerstein/Sonnhammer/Chothia ad hoc sequence weighting algorithm. This is the default. (K)(-wme in HMMER) Use the Krogh/Mitchison maximum entropy algorithm to 'weight' the sequences. This supercedes the Eddy/Mitchison/Durbin maximum discrimination algorithm, which gives almost identical weights but is less robust. ME weighting seems to give a marginal increase in sensitivity over the default GSC weights, but takes a fair amount of time. (W) (-wpb in HMMER) Use the Henikoff position-based weighting scheme. (V) (-wvoronoi in HMMER) Use the Sibbald/Argos Voronoi sequence weighting algorithm in place of the default GSC weighting. (N) (-wnone in HMMER) Turn off all sequence weighting.
B (Blosum) G (Gerstein/Sonnhammer/Chothia) K (Krogh/Mitchison) W (Henikoff) V (Sibbald/Argos Voronoi) N (None) G
-o
outfile
Re-save the starting alignment to file, in Stockholm format. The columns which were assigned to match states will be marked with x's in an RF annotation line. If either the -hand or -fast construction options were chosen, the alignment may have been slightly altered to be compatible with Plan 7 transitions, so saving the final alignment and comparing to the starting alignment can let you view these alterations. See the User's Guide for more information on this arcane side effect.
Output file
<*>.ehmmbuild
-cfile
outfile
Save the observed emission and transition counts to file after the architecture has been determined (e.g. after residues/gaps have been assigned to match, delete, and insert states). This option is used in HMMER development for generating data files useful for training new Dirichlet priors. The format of count files is documented in the User's Guide.
Output file
<*>.ehmmbuild
Associated qualifiers
"-alignfile" associated seqset qualifiers
-sbegin1
-sbegin_alignfileinteger
Start of each sequence to be used
Any integer value
0
-send1
-send_alignfileinteger
End of each sequence to be used
Any integer value
0
-sreverse1
-sreverse_alignfileboolean
Reverse (if DNA)
Boolean value Yes/No
N
-sask1
-sask_alignfileboolean
Ask for begin/end/reverse
Boolean value Yes/No
N
-snucleotide1
-snucleotide_alignfileboolean
Sequence is nucleotide
Boolean value Yes/No
N
-sprotein1
-sprotein_alignfileboolean
Sequence is protein
Boolean value Yes/No
N
-slower1
-slower_alignfileboolean
Make lower case
Boolean value Yes/No
N
-supper1
-supper_alignfileboolean
Make upper case
Boolean value Yes/No
N
-sformat1
-sformat_alignfilestring
Input sequence format
Any string
-sdbname1
-sdbname_alignfilestring
Database name
Any string
-sid1
-sid_alignfilestring
Entryname
Any string
-ufo1
-ufo_alignfilestring
UFO features
Any string
-fformat1
-fformat_alignfilestring
Features format
Any string
-fopenfile1
-fopenfile_alignfilestring
Features file name
Any string
"-hmmfile" associated outfile qualifiers
-odirectory2
-odirectory_hmmfilestring
Output directory
Any string
"-o" associated outfile qualifiers
-odirectory
string
Output directory
Any string
"-cfile" associated outfile qualifiers
-odirectory
string
Output directory
Any string
General qualifiers
-auto
boolean
Turn off prompts
Boolean value Yes/No
N
-stdout
boolean
Write first file to standard output
Boolean value Yes/No
N
-filter
boolean
Read first file from standard input, write first file to standard output
Boolean value Yes/No
N
-options
boolean
Prompt for standard and additional values
Boolean value Yes/No
N
-debug
boolean
Write debug output to program.dbg
Boolean value Yes/No
N
-verbose
boolean
Report some/full command line options
Boolean value Yes/No
Y
-help
boolean
Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose
Boolean value Yes/No
N
-warning
boolean
Report warnings
Boolean value Yes/No
Y
-error
boolean
Report errors
Boolean value Yes/No
Y
-fatal
boolean
Report fatal errors
Boolean value Yes/No
Y
-die
boolean
Report dying program messages
Boolean value Yes/No
Y
-version
boolean
Report version number and exit
Boolean value Yes/No
N
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.
Input files for usage example
File: globins50.msf
!!AA_MULTIPLE_ALIGNMENT 1.0
PileUp of: *.pep
Symbol comparison table: GenRunData:blosum62.cmp CompCheck: 6430
GapWeight: 12
GapLengthWeight: 4
pileup.msf MSF: 308 Type: P August 16, 1999 09:09 Check: 9858 ..
Name: lgb1_pea Len: 308 Check: 2200 Weight: 1.00
Name: lgb1_vicfa Len: 308 Check: 214 Weight: 1.00
Name: myg_escgi Len: 308 Check: 3961 Weight: 1.00
Name: myg_horse Len: 308 Check: 5619 Weight: 1.00
Name: myg_progu Len: 308 Check: 6401 Weight: 1.00
Name: myg_saisc Len: 308 Check: 6606 Weight: 1.00
Name: myg_lycpi Len: 308 Check: 6090 Weight: 1.00
Name: myg_mouse Len: 308 Check: 6613 Weight: 1.00
Name: myg_musan Len: 308 Check: 3942 Weight: 1.00
Name: hba_ailme Len: 308 Check: 4558 Weight: 1.00
Name: hba_prolo Len: 308 Check: 5054 Weight: 1.00
Name: hba_pagla Len: 308 Check: 5383 Weight: 1.00
Name: hba_macfa Len: 308 Check: 5135 Weight: 1.00
Name: hba_macsi Len: 308 Check: 5198 Weight: 1.00
Name: hba_ponpy Len: 308 Check: 5050 Weight: 1.00
Name: hba2_galcr Len: 308 Check: 5609 Weight: 1.00
Name: hba_mesau Len: 308 Check: 4702 Weight: 1.00
Name: hba2_bosmu Len: 308 Check: 4241 Weight: 1.00
Name: hba_erieu Len: 308 Check: 4680 Weight: 1.00
Name: hba_frapo Len: 308 Check: 3549 Weight: 1.00
Name: hba_phaco Len: 308 Check: 4440 Weight: 1.00
Name: hba_trioc Len: 308 Check: 5465 Weight: 1.00
Name: hba_ansse Len: 308 Check: 3300 Weight: 1.00
Name: hba_colli Len: 308 Check: 3816 Weight: 1.00
Name: hbad_chlme Len: 308 Check: 4571 Weight: 1.00
Name: hbad_pasmo Len: 308 Check: 6777 Weight: 1.00
Name: hbaz_horse Len: 308 Check: 7187 Weight: 1.00
Name: hba4_salir Len: 308 Check: 7329 Weight: 1.00
Name: hbb_ornan Len: 308 Check: 2667 Weight: 1.00
Name: hbb_tacac Len: 308 Check: 4356 Weight: 1.00
Name: hbe_ponpy Len: 308 Check: 3827 Weight: 1.00
Name: hbb_speci Len: 308 Check: 1556 Weight: 1.00
Name: hbb_speto Len: 308 Check: 2051 Weight: 1.00
Name: hbb_equhe Len: 308 Check: 3414 Weight: 1.00
Name: hbb_sunmu Len: 308 Check: 2927 Weight: 1.00
Name: hbb_calar Len: 308 Check: 3836 Weight: 1.00
Name: hbb_mansp Len: 308 Check: 4322 Weight: 1.00
Name: hbb_ursma Len: 308 Check: 4428 Weight: 1.00
Name: hbb_rabit Len: 308 Check: 4190 Weight: 1.00
Name: hbb_tupgl Len: 308 Check: 4185 Weight: 1.00
[Part of this file has been deleted for brevity]
lgb1_pea ~~~~~~~~
lgb1_vicfa ~~~~~~~~
myg_escgi ~~~~~~~~
myg_horse ~~~~~~~~
myg_progu ~~~~~~~~
myg_saisc ~~~~~~~~
myg_lycpi ~~~~~~~~
myg_mouse ~~~~~~~~
myg_musan ~~~~~~~~
hba_ailme ~~~~~~~~
hba_prolo ~~~~~~~~
hba_pagla ~~~~~~~~
hba_macfa ~~~~~~~~
hba_macsi ~~~~~~~~
hba_ponpy ~~~~~~~~
hba2_galcr ~~~~~~~~
hba_mesau ~~~~~~~~
hba2_bosmu ~~~~~~~~
hba_erieu ~~~~~~~~
hba_frapo ~~~~~~~~
hba_phaco ~~~~~~~~
hba_trioc ~~~~~~~~
hba_ansse ~~~~~~~~
hba_colli ~~~~~~~~
hbad_chlme ~~~~~~~~
hbad_pasmo ~~~~~~~~
hbaz_horse ~~~~~~~~
hba4_salir ~~~~~~~~
hbb_ornan ~~~~~~~~
hbb_tacac ~~~~~~~~
hbe_ponpy ~~~~~~~~
hbb_speci ~~~~~~~~
hbb_speto ~~~~~~~~
hbb_equhe ~~~~~~~~
hbb_sunmu ~~~~~~~~
hbb_calar ~~~~~~~~
hbb_mansp ~~~~~~~~
hbb_ursma ~~~~~~~~
hbb_rabit ~~~~~~~~
hbb_tupgl ~~~~~~~~
hbb_triin ~~~~~~~~
hbb_colli ~~~~~~~~
hbb_larri ~~~~~~~~
hbb1_varex ~~~~~~~~
hbb2_xentr ~~~~~~~~
hbbl_ranca ~~~~~~~~
hbb2_tricr ~~~~~~~~
glb2_mormr ~~~~~~~~
glbz_chith FGAVFAKM
hbf1_ureca VAAMK~~~
Input files for usage example 2
File: rrm.sto
# STOCKHOLM 1.0
YIS5_YEAST/33-104 IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD...
YIS1_YEAST/66-136 IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD...
RN15_YEAST/20-91 VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD...
CST2_HUMAN/18-89 VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD...
NSR1_YEAST/269-340 LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH...
IF4B_HUMAN/98-168 AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR....
TIA1_HUMAN/108-179 VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD...
PUB1_YEAST/163-234 LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD...
NAM8_YEAST/165-237 IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD...
RT19_ARATH/33-104 LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN...
NSR1_YEAST/170-241 IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE...
PES4_YEAST/93-164 LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD...
PABP_DROME/4-75 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD...
NOP4_YEAST/28-98 LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD...
ROC5_NICSY/219-290 LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD...
ROC5_NICSY/116-187 LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD...
ROC3_NICSY/99-170 LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN...
GBP2_YEAST/221-291 VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD...
PABP_SCHPO/263-333 VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD...
PABP_DROME/183-254 VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS....
PABP_DROME/92-162 VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD...
SFR3_HUMAN/12-78 VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN...
SR55_DROME/5-68 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN....
SFR1_HUMAN/17-85 IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR...
SFR2_CHICK/16-87 LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD...
ROG_HUMAN/10-81 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD...
TRA2_DROME/99-170 IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID...
ROC_HUMAN/18-82 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK....
NONA_DROME/304-369 LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD...
RU17_DROME/104-175 LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD...
TIA1_HUMAN/216-281 VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD...
TIA1_HUMAN/9-78 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD...
PUB1_YEAST/76-146 LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID...
SXL_DROME/213-285 LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD...
ELAV_DROME/250-322 LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN...
SXL_DROME/127-198 LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD...
ELV4_HUMAN/48-119 LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD...
MSSP_HUMAN/31-102 LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD...
ELAV_DROME/404-475 IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD...
SQD_DROME/138-208 IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD...
ROA1_BOVIN/106-176 IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD...
CABA_MOUSE/161-231 IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID...
SQD_DROME/58-128 LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD...
RB97_DROME/34-104 LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD...
GR10_BRANA/8-79 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND...
CABA_MOUSE/77-147 MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD...
[Part of this file has been deleted for brevity]
ROA1_BOVIN/106-176 NCEV
CABA_MOUSE/161-231 KCEI
SQD_DROME/58-128 KVDP
RB97_DROME/34-104 TVEA
GR10_BRANA/8-79 TITV
CABA_MOUSE/77-147 VIDP
SFPQ_HUMAN/373-443 TTPR
NONA_DROME/378-448 ASLR
NOP3_YEAST/127-190 PLEV
GBP2_YEAST/124-193 KLMV
U2AF_SCHPO/312-383 KLHA
U2AF_HUMAN/261-332 KLLV
NUCL_CHICK/283-352 EIKL
MODU_DROME/342-410 EWKL
RU2B_HUMAN/9-81 PMRI
RU1A_HUMAN/12-84 PMRI
PUB1_YEAST/342-407 NLRT
PTB_HUMAN/186-253 CCTL
EWS_HUMAN/363-442 KLKV
ARP2_PLAFA/364-438 YLKV
YHH5_YEAST/315-384 TIWV
PES4_YEAST/305-374 KLLV
YHC4_YEAST/348-415 TMHV
PR24_YEAST/212-284 EISV
MODU_DROME/422-484 PIFI
RNP1_YEAST/37-109 KIVI
GBP2_YEAST/351-421 SLQI
NOP4_YEAST/292-363 LIGD
MEI2_SCHPO/197-265 LLYF
IF39_YEAST/79-157 RLFL
ROF_HUMAN/113-183 YIEV
MODU_DROME/260-326 FITV
WHI3_YEAST/540-614 TVSS
CPO_DROME/453-526 PQTI
RU2B_HUMAN/153-220 AMKI
RU1A_HUMAN/210-276 NAMK
RU1A_YEAST/229-293 NDVT
SFR1_HUMAN/122-186 EGET
NOP3_YEAST/202-270 VITV
U2AG_HUMAN/67-142 PIHA
D111_ARATH/285-364 TVRA
PR24_YEAST/43-111 EIIV
MODU_DROME/177-246 VLSV
SSB1_YEAST/39-114 EIHI
RN12_YEAST/200-267 VLHI
PTB_HUMAN/61-128 PIYI
LA_HUMAN/113-182 DLLI
LA_DROME/151-225 ELLR
PR24_YEAST/119-190 TLVT
IF39_SCHPO/41-124 TFVV
//
Input files for usage example 3
File: fn3.sto
# STOCKHOLM 1.0
#=GF ID fn3
#=GF AC PF00041
#=GF DE Fibronectin type III domain
#=GF AU Sonnhammer ELL
#=GF GA 7.8 -1.0
#=GF TC 7.7 7.7
#=GF TC 7.9 0.1
#=GF AL HMM_simulated_annealing
#=GF SE Swissprot_feature_table
#=GF TP Domain
#=GF BM hmmbuild -F HMM_ls SEED
#=GF BM hmmcalibrate --seed 0 HMM_ls
#=GF BM hmmbuild -f -F HMM_fs SEED
#=GF BM hmmcalibrate --seed 0 HMM_fs
#=GF AM globalfirst
#=GF RN [1]
#=GF RM 90384924
#=GF RT Structural design and molecular evolution of a cytokine
#=GF RT receptor superfamily.
#=GF RA Bazan JF;
#=GF RL PNAS USA 1990;87:6934-6938.
#=GF RN [2]
#=GF RM 95106303
#=GF RT Tracing the spread of fibronectin type III domains in
#=GF RT bacterial glycohydrolases.
#=GF RA Little E, Bork P, Doolittle R;
#=GF RL J Mol Evol 1994;39:631-643.
#=GF RC Definition of fibronectin domains
#=GF RN [3]
#=GF RM 85284965
#=GF RT Primary structure of human fibronectin: differential
#=GF RT splicing may generate at least 10 polypeptides from a
#=GF RT single gene.
#=GF RA Kornblihtt AR, Umezawa K, Vibe-Pedersen K, Baralle FE;
#=GF RL EMBO J. 1985;4:1755-1759.
#=GF DR PROSITE; PDOC00214;
#=GF DR PRINTS; PR00014;
#=GF DR SCOP; 1ttf; sf;
#=GF DR SMART; FN3;
#=GF DR HOMSTRAD; fn3;
#=GF DC The following Pfam-B families contain sequences that according to Prodom
#=GF DC are members of this Pfam-A family.
#=GF DR PFAMB; PB001437;
#=GF DR PFAMB; PB004758;
#=GF DR PFAMB; PB007041;
#=GF DR PFAMB; PB007646;
#=GF DR PFAMB; PB012739;
#=GF DR PFAMB; PB016725;
#=GF DR PFAMB; PB016744;
[Part of this file has been deleted for brevity]
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
//
Input files for usage example 4
File: pkinase.sto
# STOCKHOLM 1.0
#=GF ID pkinase
#=GF AC PF00069
#=GF DE Protein kinase domain
#=GF AU Sonnhammer ELL
#=GF GA -57.9 -57.9
#=GF TC -58.0 -58.0
#=GF TC -57.7 -57.7
#=GF AL Clustalw
#=GF SE Unknown
#=GF TP Domain
#=GF BM hmmbuild -F HMM_ls SEED
#=GF BM hmmcalibrate --seed 0 HMM_ls
#=GF BM hmmbuild -f -F HMM_fs SEED
#=GF BM hmmcalibrate --seed 0 HMM_fs
#=GF AM byscore
#=GF RN [1]
#=GF RM 92065863
#=GF RT Protein kinase catalytic domain sequence database:
#=GF RT identification of conserved features of primary structure
#=GF RT and classification of family members.
#=GF RA Hanks SK, Quinn AM;
#=GF RL Methods Enzymol 1991;200:38-62.
#=GF RN [2]
#=GF RM 95285959
#=GF RT Protein kinases 6. The eukaryotic protein kinase
#=GF RT superfamily: kinase (catalytic) domain structure and
#=GF RT classification.
#=GF RA Hanks SK, Hunter T;
#=GF RL FASEB J 1995;9:576-596.
#=GF RN [3]
#=GF RM 97172697
#=GF RT The protein kinases of budding yeast: six score and more.
#=GF RA Hunter T, Plowman GD;
#=GF RL Trends Biochem Sci 1997;22:18-22.
#=GF DR PROSITE; PDOC00100;
#=GF DR PROSITE; PDOC00212;
#=GF DR PROSITE; PDOC00213;
#=GF DR PROSITE; PDOC00629;
#=GF DR PROSITE_PROFILE; PS50011;
#=GF DR PRINTS; PR00109;
#=GF DC Protein kinase; unclassified specificity.
#=GF DR SMART; STYKc;
#=GF DC Serine/Threonine protein kinases, catalytic domain
#=GF DR SMART; S_TKc;
#=GF DC Tyrosine kinase, catalytic domain
#=GF DR SMART; TyrKc;
#=GF DR SCOP; 1apm; sf;
#=GF DR URL; http://www.sdsc.edu/Kinases/pk_home.html;
#=GF DR HOMSTRAD; kinase;
[Part of this file has been deleted for brevity]
#=GR SAT4_YEAST/316-590 AS .....................
KKL6_YEAST/192-508 TLTRKN.QRWSINEIYESPFV
#=GR KKL6_YEAST/192-508 AS .....................
RAN1_SCHPO/18-295 PKTRI.....TLPEL..STLV
#=GR RAN1_SCHPO/18-295 AS .....................
TRKA_HUMAN/510-781 PQQRH.....SIKDVHARL..
#=GR TRKA_HUMAN/510-781 AS .....................
KSYK_PIG/364-619 VENRP.....GFVAVELRL..
#=GR KSYK_PIG/364-619 AS .....................
BFR2_HUMAN/367-643 PSQRP.....TFKQLVEDL..
#=GR BFR2_HUMAN/367-643 AS .....................
ABL1_CAEEL/311-562 PSDRP.....RFRDIHFNL..
#=GR ABL1_CAEEL/311-562 AS .....................
7LES_DROME/2209-2481 PWERP.....SFRRCYNTL..
JAK1_HUMAN/864-1137 PSNRT.....SFQNLIEGF..
#=GR JAK1_HUMAN/864-1137 AS .....................
EGFR_DROME/938-1194 AAMRP.....TFKQLTTVF..
#=GR EGFR_DROME/938-1194 AS .....................
RYK_HUMAN/327-593 PEERP.....KFQQLVQCL..
#=GR RYK_HUMAN/327-593 AS .....................
MET_HUMAN/1078-1337 AEMRP.....SFSELVSRI..
#=GR MET_HUMAN/1078-1337 AS .....................
PHY1_CERPU/1004-1282 PLKRP......SFAVICQKL.
#=GR PHY1_CERPU/1004-1282 AS .....................
M3K9_HUMAN/3-262 PHSRP.....SFTNILDQL..
#=GR M3K9_HUMAN/3-262 AS .....................
KYK2_DICDI/108-364 PNDRP.....PFTYIVNKL..
#=GR KYK2_DICDI/108-364 AS .....................
KYK1_DICDI/1289-1559 PDSRP.....TFKQIIVHL..
#=GR KYK1_DICDI/1289-1559 AS .....................
KMIL_AVIMH/82-339 REERP.....LFPQILSSI..
#=GR KMIL_AVIMH/82-339 AS .....................
KPRO_MAIZE/534-812 RSKRP.....TMEHAVQTL..
#=GR KPRO_MAIZE/534-812 AS .....................
AVR1_HUMAN/208-495 PSARL.....TALRIKKTL..
#=GR AVR1_HUMAN/208-495 AS .....................
AVR2_HUMAN/192-479 AEARL.....SAGCVGERI..
#=GR AVR2_HUMAN/192-479 AS .....................
PKN1_MYXXA/59-320 PEDRY....ASIAAFRNALQV
#=GR PKN1_MYXXA/59-320 AS .....................
KMOS_CERAE/60-338 AAQRP.....SARPLLVDL..
#=GR KMOS_CERAE/60-338 AS .....................
KR1_PRVKA/53-332 PVRRP.....SADEILNFGMW
#=GR KR1_PRVKA/53-332 AS .....................
KR1_HSV11/191-478 GALRP.....SAAELLCLPLF
#=GR KR1_HSV11/191-478 AS .....................
JAK1_HUMAN/571-833 PNQRP.....FFRAIMRDI..
HR25_YEAST/9-273 FDEKP......DYLFLARLF.
#=GR HR25_YEAST/9-273 AS .....................
#=GC seq_cons PppR......ohppllpc.ah
//
Output file format
ehmmbuild
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
Output files for usage example
File: globin.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 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf
NSEQ 50
DATE Thu Jul 15 12:00:00 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 -1085 -142 -21 -313 45 531 201 384 -1998 -644
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 -1810 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
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -68 -6528 -4832 -894 -1115 -701 -1378 * *
[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 -1039 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 1765 -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 * *
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- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Output files for usage example 2
File: myhmms
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
NSEQ 90
DATE Thu Jul 15 12:00:00 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 -1085 -142 -21 -313 45 531 201 384 -1998 -644
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 -1197 -8080 -8115 -8020 -8297 -7789 -5911 1827 -7525 -7140 1
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- -1 -11642 -12684 -894 -1115 -701 -1378 -16 *
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- -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
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
4 -1505 -5144 -1922 -558 -1842 2472 -3303 -2213 1099 -5160 -4233 372 -4738 -530 1147 168 498 -4766 -5327 -1476 4
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -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 * *
[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 -11642 -12684 -894 -1115 -701 -1378 * *
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -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 * *
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
Output files for usage example 3
File: myhmms
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
NSEQ 90
DATE Thu Jul 15 12:00:00 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 -1085 -142 -21 -313 45 531 201 384 -1998 -644
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 -1197 -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
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -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 -4276 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 * *
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- -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 * *
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- -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
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
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- -1 -11642 -12684 -894 -1115 -701 -1378 * *
10 586 1804 -6294 -631 -1627 -1671 -4374 1029 -2223 -162 1172 -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 -4233 1026 -1873 -543 -619 575 2956 -4766 -5327 -4644 17
- -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 * *
[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
C -1 -11935 -12977 -894 -1115 -701 -1378 * *
69 -8583 -7493 -8946 -9308 -409 -8830 -5009 -7467 -8865 -3133 -6867 -2231 -8684 -7580 -8224 -8080 -8432 -7625 -4255 4885 98
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C -1 -11935 -12977 -894 -1115 -701 -1378 * *
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C -1 -11935 -12977 -894 -1115 -701 -1378 * *
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C -1 -11935 -12977 -894 -1115 -701 -1378 * *
72 -1774 157 -771 -126 -5740 -2696 -247 -1555 925 -5435 -361 -242 -5015 1187 2154 813 923 -1324 1141 185 101
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E -1 -11935 -12977 -894 -1115 -701 -1378 * *
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E -1 -11935 -12977 -894 -1115 -701 -1378 * *
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E -1 -11920 -12962 -894 -1115 -357 -2190 * *
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- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
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E -14 -11935 -6734 -894 -1115 -701 -1378 * *
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C -1 -11921 -12963 -894 -1115 -373 -2135 * *
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C -733 -11935 -1329 -894 -1115 -701 -1378 * *
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C -6367 -18 -12245 -485 -1807 -3912 -99 * *
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- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
C -1 -11248 -12290 -894 -1115 -277 -2516 * *
82 68 -5329 -386 943 -1053 -34 1308 -2479 103 -1629 757 -877 1926 1130 381 -1141 -878 -1038 -5513 -1828 117
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
C -1 -11840 -12882 -894 -1115 -101 -3893 * *
83 102 -5296 -3867 1691 21 -1212 -3624 -1510 -259 -602 -1204 -1862 1786 -1626 665 -353 -181 -4888 2391 466 118
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
C -1 -11935 -12977 -894 -1115 -701 -1378 * *
84 -1211 -5433 -3815 -1455 -5755 -850 -140 -2313 -1280 -5448 -4523 -3575 -2241 -1598 -412 3271 384 -5056 -5615 -4936 119
- * * * * * * * * * * * * * * * * * * * *
C * * * * * * * * 0
//
Output files for usage example 4
File: myhmms
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
NSEQ 90
DATE Thu Jul 15 12:00:00 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 -1085 -142 -21 -313 45 531 201 384 -1998 -644
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 -1197 -8080 -8115 -8020 -8297 -7789 -5911 1827 -7525 -7140 1
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- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 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.
-f : Use -strategy option instead.
-g : Use -strategy option instead.
-s : Use -strategy option instead.
-A : Set append: "N" or append: "Y" for "hmmfile" in the ACD file instead.
-F : Always set (an existing hmmfile will be overwritten).
-amino : Sequence alignment type is specified via the ACD file.
-nucleic : Sequence alignment type is specified via the ACD file.
-informat : All common alignment formats are supported automatically.
-wblosum : Use -weighting option to specify the sequence weighting algorithm.
-wgsc : Use -weighting option to specify the sequence weighting algorithm.
-wme : Use -weighting option to specify the sequence weighting algorithm.
-wnone : Use -weighting option to specify the sequence weighting algorithm.
-wpb : Use -weighting option to specify the sequence weighting algorithm.
-wvoronoi : Use -weighting option to specify the sequence weighting algorithm.
-verbose : Use -verbosity instead.
-weighting : Sequence weighting algorithm.
-n : Use -nhmm 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.
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
Alignment input
The user must provide the full filename of an alignment for the "alignfile" ACD option, not an indirect reference to a set of sequences, e.g. a USA is NOT acceptable. This is because hmmbuild (which ehmmbuild wraps) requires an alignment and does not support USAs.
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
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
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.
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.