gethmmalignment

Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database

Syntax

AlignStruct = gethmmalignment(PFAMName) AlignStruct = gethmmalignment(PFAMAccessNumber) AlignStruct = gethmmalignment(PFAMNumber) AlignStruct = gethmmalignment(..., 'ToFile', ToFileValue, ...) AlignStruct = gethmmalignment(..., 'Type', TypeValue, ...) AlignStruct = gethmmalignment(..., 'IgnoreGaps', IgnoreGaps, ...) AlignStruct = gethmmalignment(..., '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'`.
`PFAMAccessNumber`	Character vector specifying a protein family accession number of an HMM profile record in the PFAM database. For example, `'PF00002'`.
`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.
`TypeValue`	Character vector that specifies the set of alignments returned. Choices are: `'full'` — Default. Returns all alignments that fit the HMM profile. `'seed'` — Returns only the alignments used to generate the HMM profile.
`IgnoreGapsValue`	Controls the removal of the symbols `-` and `.` from the sequence. Choices are `true` or `false` (default).
`TimeOutValue`	Connection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

Output Arguments

AlignStruct MATLAB structure array containing the multiple sequence alignment associated with an HMM profile.

Description

AlignStruct = gethmmalignment(PFAMName) searches the PFAM database (http://pfam.xfam.org/) for the HMM profile record represented by PFAMName, a protein family name, retrieves the multiple sequence alignment associated with the HMM profile, and returns AlignStruct, a MATLAB structure array, with each structure containing the following fields:

Field	Description
`Header`	Protein name
`Sequence`	Protein sequence

AlignStruct = gethmmalignment(PFAMAccessNumber) searches the PFAM database for the HMM profile record represented by PFAMAccessNumber, a protein family accession number, retrieves the multiple sequence alignment associated with the HMM profile, and returns AlignStruct, a MATLAB structure array.

AlignStruct = gethmmalignment(PFAMNumber) determines a protein family accession number from PFAMNumber, an integer, searches the PFAM database for the associated HMM profile record, retrieves the multiple sequence alignment associated with the HMM profile, and returns AlignStruct, a MATLAB structure array.

AlignStruct = gethmmalignment(..., 'PropertyName', PropertyValue, ...) calls gethmmalignment 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:

AlignStruct = gethmmalignment(..., 'ToFile', ToFileValue, ...) saves the data returned from the PFAM database to a file specified by ToFileValue.

Note

You can read a FASTA-formatted file containing PFAM data back into the MATLAB software using the fastaread function.

AlignStruct = gethmmalignment(..., 'Type', TypeValue, ...) specifies the set of alignments returned. Choices are:

'full' — Default. Returns all sequences that fit the HMM profile.
'seed' — Returns only the sequences used to generate the HMM profile.

AlignStruct = gethmmalignment(..., 'IgnoreGaps', IgnoreGaps, ...) controls the removal of the symbols - and . from the sequence. Choices are true or false (default).

AlignStruct = gethmmalignment(..., 'TimeOut', TimeOutValue, ...) sets the connection timeout (in seconds) to retrieve data from the PFAM database.

Examples

To retrieve a multiple alignment of the sequences used to train the HMM profile for global alignment to the 7-transmembrane receptor protein in the secretin family, enter:

pfamalign = gethmmalignment('PF00002','Type','seed')

pfamalign = 

  29×1 struct array with fields:

    Header
    Sequence

Version History

Introduced before R2006a