Bioinformatics Toolbox™

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(..., 'Mirror', MirrorValue, ...)
AlignStruct = gethmmalignment(..., 'IgnoreGaps', IgnoreGaps, ...)

Arguments

Return Values

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:

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

Bioinformatics Toolbox™ functions: fastaread, gethmmprof, gethmmtree, multialignread, pfamhmmread

getgeodata

gethmmprof