HMMERCONVERT*

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
RELATED PROGRAMS
RESTRICTIONS
CONSIDERATIONS
COMMAND-LINE SUMMARY
ACKNOWLEDGEMENT
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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HmmerConvert converts profile hidden Markov model files into different profile formats.

DESCRIPTION

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HmmerConvert provides a GCG interface to the hmmconvert program of Dr. Sean Eddy's HMMER package. It allows you to access most of hmmconvert's parameters from the GCG command line.

HmmerConvert allows you to manipulate profile HMM files in several ways. By default, a profile HMM is created as an ASCII text file, but it can also exist in a binary format, which can save disk space if you have a large HMM database file. HmmerConvert allows you to convert your profile HMM between these two formats. It also allows you to convert your profile HMM into a standard profile, which can be used as input to programs such as ProfileSearch and ProfileGap. Lastly, it allows you to append a profile HMM file onto an existing profile HMM file, or to replace an existing profile HMM file with another.

EXAMPLE

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Here is a session using HmmerConvert to convert the hidden Markov model file created in the HmmerBuild example session into a GCG profile:


% hmmerconvert HMMERCONVERT what profile HMM ? hsp70.hmm_g Into which type of file ? A ASCII HMM format B Binary HMM format P Profile format E Append this profile HMM to an existing file O Overwrite an existing file with this profile HMM Choose a type (* A *) : p Converting to GCG profile. What should the output file be called (* hmmerconvert.prf *) ? Creating temp file for input to hmmconvert. Calling hmmconvert to perform analysis ... hmmconvert - convert between profile HMM file formats HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input HMM file: /usr/users/share/smith/hsp70.hmm_g Output HMM file: /usr/users/share/smith/hmmerconvert.prf Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted hsp70 1 HMM(s) converted and written to /usr/users/share/smith/hmmerconvert.prf %

OUTPUT

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Here is some of the output file:


!!AA_PROFILE 1.0
(Peptide) HMMCONVERT v2.1.1 Length: 677 hsp70||
   Profile converted from a profile HMM using HMMER v2.1.1 emulation.
   Use -nonor -noave -gap=10 -len=1 with profilesearch and friends
      to get the closest approximation to HMMER bit scores.
   WARNING: There is a loss of information in this conversion.
      Neither the scores nor even the rank order of hits will be precisely
      preserved in a comparison of HMMER hmmsearch to GCG profilesearch.
      The profile score is an approximation of the (single-hit) HMMER score.

Cons    A     C     D     E     F     G     H     I     K     L ...  Gap   Len
 ..
 K     46  -155   -25    69  -179   -35     0  -148   115  -153 ...  100   100
 V     19  -138   -35    50  -160   -50    -6  -126    27  -137 ...   66   111

/////////////////////////////////////////////////////////////////////////////////

 E    -68  -172     1   270  -183  -138   -31  -137     2  -149 ...   62   111
 V    -59   -73  -223  -200  -121  -177  -162    52  -177   -63 ...   62   111
 D   -124  -248   348    21  -312   -28   -82  -308  -103  -306 ...   62   111
 *   1450   151  1131  1249   603  1265   278  1040  1234  1320 ...

INPUT FILES

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HmmerConvert requires as its only input a profile HMM file containing one or more profile HMMs.

RELATED PROGRAMS

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PileUp creates a multiple sequence alignment from a group of related sequences. LineUp is a multiple sequence editor used to create multiple sequence alignments. Pretty displays multiple sequence alignments.

ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for sequences with similarity to the group of aligned sequences. ProfileSegments displays optimal alignments between each sequence in the ProfileSearch output list and the group of aligned sequences (represented by the profile consensus). ProfileGap makes optimal alignments between one or more sequences and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.

HmmerBuild makes a profile hidden Markov model from a multiple sequence alignment. HmmerAlign aligns one or more sequences to a profile HMM. HmmerPfam searches a database of profile HMMs with a sequence query in order to identify known domains within the sequence. HmmerSearch uses a profile HMM as a query to search a sequence database for sequences similar to the original aligned sequences. HmmerCalibrate calibrates a hidden Markov model so that database searches using it as a query will be more sensitive. HmmerIndex creates a binary GSI ("generic sequence index") for a database of profile HMMs. HmmerFetch retrieves a profile hidden Markov model by name from an indexed database of profile HMMs. HmmerEmit randomly generates sequences that match a profile HMM. HmmerConvert converts between different profile HMM file formats and from profile HMM to GCG profile file format.

MEME finds conserved motifs in a group of unaligned sequences and saves these motifs as a set of profiles. You can search a database of sequences with these profiles using the MotifSearch program.

RESTRICTIONS

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HmmerConvert will successfully append a binary format profile HMM file to an ASCII text format file, by converting the binary profile HMM into an ASCII format profile HMM. The resulting profile HMM database is valid. But it also will append an ASCII text file to a binary format file without converting it, and the resulting file will be unusable by other programs in the HMMER package. HmmerConvert also lets you create mixed nucleic and protein profile HMM databases, which will be unusable by other programs in the HMMER package as well.

CONSIDERATIONS

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When converting a profile HMM into a GCG profile, information is lost. Therefore the list of best hits obtained from ProfileSearch using this profile as a query may differ from the list of best hits obtained from HmmerSearch using the original profile HMM as the query.

If you are appending a profile HMM file onto an existing HMM file, make sure that the files are in the same format (ASCII text or binary). Mixed format profile HMM database files cannot be used by other programs in the HMMER package.

HmmerPfam searches a binary profile HMM database more quickly than the same database in ASCII text format.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % hmmerconvert [-INfile1=]hsp70.hmm_g -Default

Prompted Parameters:

[-OUTfile=]hmmerconvert.hmm sets the primary output filename

-MENu=a converts file to HMMER2 ASCII file b converts file to HMMER2 binary file p converts file to GCG profile format file e appends the file to the output file instead of creating a new file o overwrites the output file

Local Data Files: None

Optional Parameters:

-NOMONitor suppresses the screen monitor

ACKNOWLEDGEMENT

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The programs comprising the HMMER package are designed and implemented by Dr. Sean Eddy of the Washington University School of Medicine, St. Louis, Missouri. The GCG front-end programs were written by Christiane van Schlun in collaboration with Dr. Eddy.

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

Following some of the parameters described below is a short expression in parentheses. These are the names of the corresponding parameters used in the native HMMER package. Some of the GCG parameters are identical to the original HMMER parameters, others have been changed to fit GCG's conventions.

-MENu=A (-a -b -p -A -F)

specifies the action to perform. You can convert the file into a new file in one of the following formats: HMMER 2 ASCII format (A), HMMER 2 binary format (B), GCG profile format (P). You can also change an existing file by appending the input file to the existing file (E) or by overwriting the existing file (O). Unless -MENu is set to E or O, HmmerConvert will not alter existing files.

-NOMONitor

suppresses the display of the program's progress on the screen.

Printed: February 5, 2001 11:37 (1162)

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