gethmmprof

Retrieve hidden Markov model (HMM) profile from PFAM database

Syntax

HMMStruct = gethmmprof(PFAMName) HMMStruct = gethmmprof(PFAMNumber) HMMStruct = gethmmprof(..., 'ToFile', ToFileValue, ...) HMMStruct = gethmmprof(..., 'Mode', ModeValue, ...) HMMStruct = gethmmprof(..., 'TimeOut', TimeOutValue, ...)

Input Arguments

`PFAMName`	Character vector specifying a protein family name (unique identifier) of an HMM profile record in the PFAM database. For example, `'7tm_2'`.
`PFAMNumber`	Integer specifying a protein family number of an HMM profile record in the PFAM database. For example, `2` is the protein family number for the protein family `'PF00002'`.
`ToFileValue`	Character vector specifying a file name or a path and file name for saving the data. If you specify only a file name, that file will be saved in the MATLAB^® Current Folder.
`ModeValue`	Character vector that specifies the returned alignment mode. Choices are: `'ls'` — Default. Global alignment mode. `'fs'` — Local alignment mode.
`TimeOutValue`	Connection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

Output Arguments

HMMStruct MATLAB structure containing information for an HMM profile retrieved from the PFAM database.

Description

Note

gethmmprof retrieves information from PFAM-HMM profiles, from file format version HMMER2.0 to HMMER3/f.

HMMStruct = gethmmprof(PFAMName) searches the PFAM database (http://pfam.xfam.org/) for the record represented by PFAMName (a protein family name), retrieves the HMM profile information, and stores it in HMMStruct, a MATLAB structure containing the following fields corresponding to parameters of an HMM profile.

Field	Description
`Name`	The protein family name (unique identifier) of the HMM profile record in the PFAM database.
`PfamAccessionNumber`	The protein family accession number of the HMM profile record in the PFAM database.
`ModelDescription`	Description of the HMM profile.
`ModelLength`	The length of the profile (number of MATCH states).
`Alphabet`	The alphabet used in the model, `'AA'` or `'NT'`. Note `AlphaLength` is 20 for `'AA'` and 4 for `'NT'`.
`MatchEmission`	Symbol emission probabilities in the MATCH states. The format is a matrix of size `ModelLength`-by-`AlphaLength`, where each row corresponds to the emission distribution for a specific MATCH state.
`InsertEmission`	Symbol emission probabilities in the INSERT state. The format is a matrix of size `ModelLength`-by-`AlphaLength`, where each row corresponds to the emission distribution for a specific INSERT state.
`NullEmission`	Symbol emission probabilities in the MATCH and INSERT states for the NULL model. The format is a 1-by-`AlphaLength` row vector. Note NULL probabilities are also known as the background probabilities.
`BeginX`	BEGIN state transition probabilities. Format is a 1-by-`(ModelLength + 1)` row vector: [B->D1 B->M1 B->M2 B->M3 .... B->Mend]
`MatchX`	MATCH state transition probabilities. Format is a 4-by-`(ModelLength - 1)` matrix: [M1->M2 M2->M3 ... M[end-1]->Mend; M1->I1 M2->I2 ... M[end-1]->I[end-1]; M1->D2 M2->D3 ... M[end-1]->Dend; M1->E M2->E ... M[end-1]->E ]
`InsertX`	INSERT state transition probabilities. Format is a 2-by-`(ModelLength - 1)` matrix: [ I1->M2 I2->M3 ... I[end-1]->Mend; I1->I1 I2->I2 ... I[end-1]->I[end-1] ]
`DeleteX`	DELETE state transition probabilities. Format is a 2-by-`(ModelLength - 1)` matrix: [ D1->M2 D2->M3 ... D[end-1]->Mend ; D1->D2 D2->D3 ... D[end-1]->Dend ]
`FlankingInsertX`	Flanking insert states (N and C) used for LOCAL profile alignment. Format is a 2-by-2 matrix: [N->B C->T ; N->N C->C]
`LoopX`	Loop states transition probabilities used for multiple hits alignment. Format is a 2-by-2 matrix: [E->C J->B ; E->J J->J]
`NullX`	Null transition probabilities used to provide scores with log-odds values also for state transitions. Format is a 2-by-1 column vector: [G->F ; G->G]

HMMStruct = gethmmprof(PFAMNumber) determines a protein family accession number from PFAMNumber (an integer), searches the PFAM database for the associated record, retrieves the HMM profile information, and stores it in HMMStruct, a MATLAB structure.

HMMStruct = gethmmprof(..., 'PropertyName', PropertyValue, ...) calls gethmmprof with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

HMMStruct = gethmmprof(..., 'ToFile', ToFileValue, ...) saves the data returned from the PFAM database in a file specified by ToFileValue.

Note

You can read an HMM-formatted file back into the MATLAB software using the pfamhmmread function.

HMMStruct = gethmmprof(..., 'Mode', ModeValue, ...) specifies the returned alignment mode. Choices are:

'ls' (default) — Global alignment mode.
'fs' — Local alignment mode.

For more information on HMM profile models, see HMM Profile Model.

HMMStruct = gethmmprof(..., 'TimeOut', TimeOutValue, ...) sets the connection timeout (in seconds) to retrieve data the PFAM database.

Examples

To retrieve a hidden Markov model (HMM) profile for the global alignment of the 7-transmembrane receptor protein in the secretin family, enter:

hmm = gethmmprof('7tm_2')

hmm = 

  struct with fields:

                   Name: '7tm_2'
    PfamAccessionNumber: 'PF00002.21'
       ModelDescription: '7 transmembrane receptor (Secretin family)'
            ModelLength: 241
               Alphabet: 'AA'
          MatchEmission: [241×20 double]
         InsertEmission: [241×20 double]
           NullEmission: [1×20 double]
                 BeginX: [242×1 double]
                 MatchX: [240×4 double]
                InsertX: [240×2 double]
                DeleteX: [240×2 double]
        FlankingInsertX: [2×2 double]
                  LoopX: [2×2 double]
                  NullX: [2×1 double]

Version History

Introduced before R2006a