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

Syntax

Input Arguments

PFAMName	String specifying a protein family name (unique identifier) of an HMM profile record in the PFAM database. For example, '7tm_2'.
PFAMAccessNumber	String 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	String 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	String 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.
MirrorValue	String that specifies a Web database. Choices are: 'Sanger' (default) 'Janelia'
IgnoreGapsValue	Controls the removal of the symbols - and . from the sequence. Choices are true or false (default).

Output Arguments

AlignStruct

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

Description

AlignStruct = gethmmalignment(PFAMName) searches the PFAM database 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(..., 'Mirror', MirrorValue, ...) specifies a Web database. Choices are:

• 'Sanger' (default)

• 'Janelia'

You can reach other mirror sites by passing the complete URL to the fastaread function.

Note   These mirror sites are maintained separately and may have slight variations.

For more information about the PFAM database, see:

http://pfam.sanger.ac.uk
http://pfam.janelia.org/

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

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 either of the following:

pfamalign = gethmmalignment(2,'Type','seed')

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

pfamalign = 

32x1 struct array with fields:
    Header
    Sequence

See Also

fastaread | gethmmprof | gethmmtree | multialignread | multialignwrite | pfamhmmread

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