EMBOSS: ehmmpfam

ehmmpfam

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Function

Search one or more sequences against 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:
ehmmpfam [options] hmmfile seqfile outfile

The outfile parameter is new to EMBASSY HMMER.

hmmpfam reads a sequence file and compares each sequence in it, one at a time, against all the HMMs in a file looking for signifcantly similar sequence matches. hmmfile will be looked for first in the current working directory, then in a directory named by the environment variable HMMERDB. This lets administrators install HMM library(s) such as Pfam in a common location. There is a separate output report (written to file for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the -domE and -domT options.

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 ehmmpfam

% ehmmpfam ../ehmmcalibrate-keep2/myhmmso 7LES_DROME myhmmso.ehmmpfam -A 10 -E 10 Search one or more sequences against an HMM database. /shared/software/bin/hmmpfam -A 10 -E 10.000000 -T -1000000.000000 -Z 59021 --domE 1000000.000000 --domT -1000000.000000 --informat FASTA ../ehmmcalibrate-keep2/myhmmso ./ehmmpfam-1234567890.1234

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).

Search one or more sequences against an HMM database. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-hmmfile] infile File of HMMs. [-seqfile] seqall File of sequences. -a integer [100] Limits the alignment output to the best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files. (Any integer value) -e float [10.] Set the E-value cutoff for the per-sequence ranked hit list to , where is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown. (Any numeric value) [-outfile] outfile [*.ehmmpfam] There is a separate output report for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. Additional (Optional) qualifiers: -nuc boolean [N] Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can't reliably determine the correct 'alphabet' by itself. -t float [-1000000.] Set the bit score cutoff for the per-sequence ranked hit list to , where is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown. (Any numeric value) -z integer [59021] Calculate the E-value scores as if we had seen a sequence database of sequences. The default is arbitrarily set to 59021, the size of Swissprot 34. (Any integer value) Advanced (Unprompted) qualifiers: -acc boolean [N] Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database. -compat boolean [N] Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten. -cpu integer [0] Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems). (Any integer value) -cutga boolean [N] Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT -domT , but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn't work. -cuttc boolean [N] Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT -domT , but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn't work. -cutnc boolean [N] Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT -domT , but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn't work. -dome float [1000000.] Set the E-value cutoff for the per-domain ranked hit list to , where is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. (Any numeric value) -domt float [-1000000.] Set the bit score cutoff for the per-domain ranked hit list to , where is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users' Guide for more detail. (Any numeric value) -forward boolean [N] Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however. -nulltwo boolean [N] Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases --null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through. -pvm boolean [N] Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function. -xnu boolean [N] Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model. Associated qualifiers: "-seqfile" associated qualifiers -sbegin2 integer Start of each sequence to be used -send2 integer End of each sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -scircular2 boolean Sequence is circular -squick2 boolean Read id and sequence only -sformat2 string Input sequence format -iquery2 string Input query fields or ID list -ioffset2 integer Input start position offset -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 string Features file name "-outfile" associated qualifiers -odirectory3 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

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-hmmfile]
(Parameter 1) infile File of HMMs. Input file Required

[-seqfile]
(Parameter 2) seqall File of sequences. Readable sequence(s) Required

-a integer Limits the alignment output to the <n> best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files. Any integer value 100

-e float Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown. Any numeric value 10.

[-outfile]
(Parameter 3) outfile There is a separate output report for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. Output file <*>.ehmmpfam

Additional (Optional) qualifiers

-nuc boolean Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can't reliably determine the correct 'alphabet' by itself. Boolean value Yes/No No

-t float Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown. Any numeric value -1000000.

-z integer Calculate the E-value scores as if we had seen a sequence database of <n> sequences. The default is arbitrarily set to 59021, the size of Swissprot 34. Any integer value 59021

Advanced (Unprompted) qualifiers

-acc boolean Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database. Boolean value Yes/No No

-compat boolean Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten. Boolean value Yes/No No

-cpu integer Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems). Any integer value 0

-cutga boolean Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT <GA1> -domT <GA2>, but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn't work. Boolean value Yes/No No

-cuttc boolean Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT <TC1> -domT <TC2>, but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn't work. Boolean value Yes/No No

-cutnc boolean Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT <NC1> -domT <NC2>, but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn't work. Boolean value Yes/No No

-dome float Set the E-value cutoff for the per-domain ranked hit list to <x>, where <x> is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Any numeric value 1000000.

-domt float Set the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users' Guide for more detail. Any numeric value -1000000.

-forward boolean Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however. Boolean value Yes/No No

-nulltwo boolean Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases --null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through. Boolean value Yes/No No

-pvm boolean Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function. Boolean value Yes/No No

-xnu boolean Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model. Boolean value Yes/No No

Associated qualifiers

"-seqfile" associated seqall qualifiers

-sbegin2
-sbegin_seqfile integer Start of each sequence to be used Any integer value 0

-send2
-send_seqfile integer End of each sequence to be used Any integer value 0

-sreverse2
-sreverse_seqfile boolean Reverse (if DNA) Boolean value Yes/No N

-sask2
-sask_seqfile boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide2
-snucleotide_seqfile boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein2
-sprotein_seqfile boolean Sequence is protein Boolean value Yes/No N

-slower2
-slower_seqfile boolean Make lower case Boolean value Yes/No N

-supper2
-supper_seqfile boolean Make upper case Boolean value Yes/No N

-scircular2
-scircular_seqfile boolean Sequence is circular Boolean value Yes/No N

-squick2
-squick_seqfile boolean Read id and sequence only Boolean value Yes/No N

-sformat2
-sformat_seqfile string Input sequence format Any string

-iquery2
-iquery_seqfile string Input query fields or ID list Any string

-ioffset2
-ioffset_seqfile integer Input start position offset Any integer value 0

-sdbname2
-sdbname_seqfile string Database name Any string

-sid2
-sid_seqfile string Entryname Any string

-ufo2
-ufo_seqfile string UFO features Any string

-fformat2
-fformat_seqfile string Features format Any string

-fopenfile2
-fopenfile_seqfile string Features file name Any string

"-outfile" associated outfile qualifiers

-odirectory3
-odirectory_outfile 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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-hmmfile] (Parameter 1)	infile	File of HMMs.	Input file	Required
[-seqfile] (Parameter 2)	seqall	File of sequences.	Readable sequence(s)	Required
-a	integer	Limits the alignment output to the <n> best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files.	Any integer value	100
-e	float	Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown.	Any numeric value	10.
[-outfile] (Parameter 3)	outfile	There is a separate output report for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains.	Output file	<>*.ehmmpfam
Additional (Optional) qualifiers
-nuc	boolean	Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can't reliably determine the correct 'alphabet' by itself.	Boolean value Yes/No	No
-t	float	Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown.	Any numeric value	-1000000.
-z	integer	Calculate the E-value scores as if we had seen a sequence database of <n> sequences. The default is arbitrarily set to 59021, the size of Swissprot 34.	Any integer value	59021
Advanced (Unprompted) qualifiers
-acc	boolean	Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database.	Boolean value Yes/No	No
-compat	boolean	Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten.	Boolean value Yes/No	No
-cpu	integer	Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).	Any integer value	0
-cutga	boolean	Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT <GA1> -domT <GA2>, but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn't work.	Boolean value Yes/No	No
-cuttc	boolean	Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT <TC1> -domT <TC2>, but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn't work.	Boolean value Yes/No	No
-cutnc	boolean	Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT <NC1> -domT <NC2>, but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn't work.	Boolean value Yes/No	No
-dome	float	Set the E-value cutoff for the per-domain ranked hit list to <x>, where <x> is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list.	Any numeric value	1000000.
-domt	float	Set the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users' Guide for more detail.	Any numeric value	-1000000.
-forward	boolean	Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however.	Boolean value Yes/No	No
-nulltwo	boolean	Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases --null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through.	Boolean value Yes/No	No
-pvm	boolean	Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function.	Boolean value Yes/No	No
-xnu	boolean	Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model.	Boolean value Yes/No	No
Associated qualifiers
"-seqfile" associated seqall qualifiers
-sbegin2 -sbegin_seqfile	integer	Start of each sequence to be used	Any integer value	0
-send2 -send_seqfile	integer	End of each sequence to be used	Any integer value	0
-sreverse2 -sreverse_seqfile	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask2 -sask_seqfile	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide2 -snucleotide_seqfile	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein2 -sprotein_seqfile	boolean	Sequence is protein	Boolean value Yes/No	N
-slower2 -slower_seqfile	boolean	Make lower case	Boolean value Yes/No	N
-supper2 -supper_seqfile	boolean	Make upper case	Boolean value Yes/No	N
-scircular2 -scircular_seqfile	boolean	Sequence is circular	Boolean value Yes/No	N
-squick2 -squick_seqfile	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat2 -sformat_seqfile	string	Input sequence format	Any string
-iquery2 -iquery_seqfile	string	Input query fields or ID list	Any string
-ioffset2 -ioffset_seqfile	integer	Input start position offset	Any integer value	0
-sdbname2 -sdbname_seqfile	string	Database name	Any string
-sid2 -sid_seqfile	string	Entryname	Any string
-ufo2 -ufo_seqfile	string	UFO features	Any string
-fformat2 -fformat_seqfile	string	Features format	Any string
-fopenfile2 -fopenfile_seqfile	string	Features file name	Any string
"-outfile" associated outfile qualifiers
-odirectory3 -odirectory_outfile	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.

ehmmpfam reads any normal sequence USAs.

Input files for usage example

File: ../ehmmcalibrate-keep2/myhmmso

HMMER2.0  [2.3.2]
NAME  rrm
LENG  77
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /home/pmr/local/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   /home/pmr/local/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-keep4/myhmms
NSEQ  90
DATE  Mon Jul 15 12:00:00 2013
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 
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  -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
     -   -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  -4233    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  -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      *      * 
     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  -4224    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  -4224   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   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


  [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  -6953  -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  -2618  -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  -3503   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  -2044  -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   1713  -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  -3851   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  -3616  -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   1434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *      *      0 
//

File: 7LES_DROME

ID   7LES_DROME     STANDARD;      PRT;  2554 AA.
AC   P13368;
DT   01-JAN-1990 (Rel. 13, Created)
DT   01-JAN-1990 (Rel. 13, Last sequence update)
DT   01-NOV-1997 (Rel. 35, Last annotation update)
DE   SEVENLESS PROTEIN (EC 2.7.1.112).
GN   SEV.
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
OC   Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=CANTON-S;
RX   MEDLINE; 88282538.
RA   BASLER K., HAFEN E.;
RT   "Control of photoreceptor cell fate by the sevenless protein requires
RT   a functional tyrosine kinase domain.";
RL   Cell 54:299-311(1988).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   STRAIN=OREGON-R;
RX   MEDLINE; 88329706.
RA   BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
RT   "Nucleotide sequence and structure of the sevenless gene of
RT   Drosophila melanogaster.";
RL   Genes Dev. 2:620-634(1988).
RN   [3]
RP   IDENTIFICATION OF FN-III REPEATS.
RX   MEDLINE; 90199889.
RA   NORTON P.A., HYNES R.O., RESS D.J.G.;
RT   "Sevenless: seven found?";
RL   Cell 61:15-16(1990).
CC   -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
CC       INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
CC       LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
CC       SURFACE OF THE NEIGHBORING R8 CELL.
CC   -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
CC       PROTEIN TYROSINE PHOSPHATE.
CC   -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
CC   -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
CC       PROTEIN KINASES. SEVENLESS SUBFAMILY.
CC   -!- SIMILARITY: CONTAINS 7 FIBRONECTIN TYPE III-LIKE DOMAINS.
CC   -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
CC       NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
CC       NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its


  [Part of this file has been deleted for brevity]

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

Output file format

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

Output files for usage example

File: myhmmso.ehmmpfam

hmmpfam - search one or more sequences against 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:                 ../ehmmcalibrate-keep2/myhmmso
Sequence file:            ./ehmmpfam-1234567890.1234
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: 7LES_DROME
Accession:      [none]
Description:    P13368 SEVENLESS PROTEIN (EC 2.7.1.112).

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
pkinase  Protein kinase domain                          314.6    1.2e-90   1
fn3      Fibronectin type III domain                    176.6      4e-49   6

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
fn3        1/6     437   522 ..     1    84 []    48.3  1.7e-10
fn3        2/6     825   914 ..     1    84 []    13.4     0.09
fn3        3/6    1292  1389 ..     1    84 []    15.9     0.05
fn3        4/6    1799  1891 ..     1    84 []    63.5  4.5e-15
fn3        5/6    1899  1978 ..     1    84 []    15.2     0.06
fn3        6/6    1993  2107 ..     1    84 []    20.3    0.018
pkinase    1/1    2209  2483 ..     1   294 []   314.6  1.2e-90

Alignments of top-scoring domains:
fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 1.7e-10
                CS    C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
                   *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
                      P saP   + +++ ++ l ++W p +  ngpi+gY++++ +++ g+ 
  7LES_DROME   437    PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482  

                CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
                   wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                   + e+ vp    sy+++ L++gt+Y++ +  +n +G+Gp     
  7LES_DROME   483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA    522  

fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 0.09
                CS    CCCCCEEEEEECCTTCCEEEEECCC       CCCCCCCEEEEE.EC
                   *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
                       ++P  l++   ++  + +sW+ p++++ ++ + +   +Ye+++  +
  7LES_DROME   825    GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869  

                CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC  CCCC   
                   knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*


  [Part of this file has been deleted for brevity]

                CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
                   eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                   +++v g+ t ++++ L+P t+Y+ r+    ++++G++    
  7LES_DROME  1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL    1978 

fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 0.018
                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC 
                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
                      Ps+P+ ++ + + +  ++++W++++++++pi  Y+++   ++++  +
  7LES_DROME  1993    PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038 

                CS                            CCCCEEECCCC CECECCEEEEE
                   ...........................wneltvpgttt.sytltgLkPgt
                   +++++++++++++ ++ +  +++   ++++l+  +tt  s++++ L   +
  7LES_DROME  2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088 

                CS CCCCEEEEEE CCC CCCC   
                   eYevrVqAvn.ggG.GpeS<-*
                      +rV+A++ ++G Gp+S   
  7LES_DROME  2089 LLLFRVRARSlEHGwGPYS    2107 

pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 1.2e-90
                   *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
                      ++ll+ lG+G+fG+Vy++++k+++++  ++VA+K l+k+++++ e  
  7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253 

                   flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
                   +l E+q++ +++H+NIvrl g++  + +++ l+mE+me GdL++ylr+ +
  7LES_DROME  2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302 

                   ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
                    +++++++++  ls  e++ ++ ++++G +YL+++++vHRDL+ +N+L++
  7LES_DROME  2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352 

                   en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
                   e +++++++ tvKi+DFGLAr++++++++++ + +  p+++m+PE  l +
  7LES_DROME  2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401 

                   rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
                     +++++DvW++Gv+++E+lt g                         ++
  7LES_DROME  2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426 

                   PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
                   P+         ++ +e+++++k+ g+rl +p+ c e l++Ll  c++ DP
  7LES_DROME  2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468 

                   skRpGsatakeilnhpwf<-*
                   ++Rp   +++ + n +     
  7LES_DROME  2469 WERP---SFRRCYNTLHA    2483 

//

Data files

None.

Notes

1. Command-line arguments

The following original HMMER options are not supported:

-h         : Use -help to get help information instead.
-informat  : All common sequence file formats are supported automatically.
-n         : Use -nuc instead (-n causes problems for GUI developers)

The following additional options are provided:

-outfile   : Output file with HMM.

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

Disk space requirements

ehmmpfam makes a temporary local copy of its input sequence data. You must ensure there is sufficient disk space for this in the directory that ehmmpfam is run.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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
ehmmindex	Create a binary SSI index for an HMM database
ehmmsearch	Search a sequence database with a profile HMM
libgen	Generate discriminating elements from alignments
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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author. Jon Ison
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.

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Alignment and sequence formats

Compressed input files

Input files for usage example

File: ../ehmmcalibrate-keep2/myhmmso

File: 7LES_DROME

Output file format

Output files for usage example

File: myhmmso.ehmmpfam

Data files

Notes

1. Command-line arguments

2. Installing EMBASSY HMMER

3. Installing original HMMER

4. Setting up HMMER

5. Getting help

References

Warnings

Types of input data

Environment variables

Disk space requirements

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments