HMMERFETCH*

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

FUNCTION

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HmmerFetch retrieves a profile hidden Markov model (HMM) from a database of profile HMMs that has been indexed by HmmerIndex.

DESCRIPTION

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HmmerFetch provides a GCG interface to the hmmfetch program of Dr. Sean Eddy's HMMER package. It allows you to access most of hmmfetch's parameters from the GCG command line. The database must have been previously indexed with HmmerIndex.

Two profile HMM databases for protein families are available with the Wisconsin Package: Pfam and PfamFrag. Indexes for these have already been created, so they can be used with HmmerFetch without any further processing.

EXAMPLE

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Here is a session using HmmerFetch to retrieve from the Pfam database a profile HMM representing a heat shock protein family:


% hmmerfetch HMMERFETCH which profile HMM ? HSP70 from which HMM database (* Pfam.hmmdb *) ? What output name (* HSP70.hmm_g *)? Creating temp file for input to hmmfetch . Calling hmmfetch to perform analysis ... %

OUTPUT

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Here is some of the output file:


HMMER2.0
NAME  HSP70
ACC   PF00012
DESC  Hsp70 protein
LENG  621
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   hmmbuild -F HMM.ann SEED.ann
COM   hmmcalibrate --seed 0 HMM.ann
NSEQ  34
DATE  Tue May  4 18:13:41 1999
CKSUM 8575
GA    -80.0 -80.0
TC    -72.0 -72.0
NC    -83.0 -83.0
XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158  ...  -1998   -644
EVD   -531.700623   0.081970
HMM        A      C      D      E      F      G      H  ...      W      Y
         m->m   m->i   m->d   i->m   i->i   d->m   d->d
   b->m   m->e
         -126      *  -3585
     1   1571  -1709  -4201  -3697  -1975  -3272  -2660 ...  -2595  -2243     1
     -   -149   -500    233     43   -381    399    106 ...  -294   -249
     -     -6  -8606  -9649   -894  -1115   -701  -1378   -126      *
     2   -645  -2273  -5213  -4741    224  -4752  -4004 ...  -3631  -3277     2
     -   -149   -500    233     43   -381    399    106 ...  -294   -249
     -     -6  -8606  -9649   -894  -1115   -701  -1378      *      *

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

   619    406  -1186  -3444   -148  -1142  -2846  -1705 ...  -1640   1325   686
     -   -149   -500    233     43   -381    399    106 ...  -294   -249
     -     -6  -8562  -9604   -894  -1115   -701  -1378      *      *
   620  -1249  -1701  -1826  -1260  -1730   -806    231 ...  -2069   3639   687
     -   -149   -500    233     43   -381    399    106 ...  -294   -249
     -     -6  -8562  -9604   -894  -1115   -701  -1378      *      *
   621   1064  -2653     83   1302  -2973   -439   -803 ...  -2836  -2150   688
     -      *      *      *      *      *      *      * ...      *      *
     -      *      *      *      *      *      *      *      *      0
//

INPUT FILES

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HmmerFetch has two required inputs: an indexed database of profile HMMs and the name of a profile HMM that is present in that database. Profile HMM databases supplied with the Wisconsin Package are Pfam and PfamFrag. They each contain profile HMMs for a large number of protein families. The profile HMMs in these databases were made from the same sequence alignments, but with different parameters: the profile HMMs in Pfam are built to perform global alignments with respect to the model, while the profile HMMs in PfamFrag are designed to perform local alignments with respect to the model.

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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A profile HMM database must be indexed with HmmerIndex before it can be used with HmmerFetch. The index must be stored in the same directory as the database.

HmmerFetch differs from Fetch in that it is case sensitive. If a model is named OmpA, you must type its name as OmpA. HmmerFetch will not be able to find it if you type ompa, ompA, Ompa, etc.

HmmerFetch can only retrieve a single profile HMM model at a time. It does not accept a wildcard specification or a list of models to be fetched.

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: % hmmerfetch [-INfile1=]HSP70 [-INfile2=]Pfam.hmmdb -Default

Prompted Parameters:

[-OUTfile=]HSP70.hmm_g sets primary output filename

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.

Pfam - A database of protein domain family alignments and HMMs Copyright (C) 1996-2000 The Pfam Consortium.

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.

-NOMONitor

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

Printed: February 5, 2001 11:36 (1162)

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