gethmmtree - Retrieve phylogenetic tree data 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'.
PFAMAccessionNumber	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 PF0002.
ToFileValue	Property to specify the location and file name for saving data. Enter either a file name or a path and file name supported by your system (ASCII text file).
TypeValue	String that specifies which alignments to include in the tree. Choices are: 'seed' — Returns a tree with only the alignments used to generate the HMM model. 'full' (default) — Returns a tree with all of the alignments that match the model.

Output Arguments

Tree	An object containing a phylogenetic tree representative of the protein family.

Description

Tree = gethmmtree(PFAMName) searches the PFAM database for the record represented by PFAMName, a protein family name, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(PFAMAccessionNumber) searches the PFAM database for the record represented by PFAMAccessionNumber, a protein family accession number, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(PFAMNumber) determines a protein family accession number from PFAMNumber, an integer, searches the PFAM database for the associated record, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(...'PropertyName', PropertyValue, ...) calls gethmmtree 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:

Tree = gethmmtree(...'ToFile', ToFileValue, ...) saves the data returned from the PFAM database in the file ToFileValue.

Tree = gethmmtree(...'Type', TypeValue, ...) specifies which alignments to include in the tree. Choices for TypeValue are:

• 'seed' — Returns a tree with only the alignments used to generate the HMM model.

• 'full' (default) — Returns a tree with all of the alignments that match the model.

Examples

Enter either of the following to retrieve phylogenetic tree data from the multiple-aligned sequences used to train the HMM profile model for global alignment. The PFAM accession number PF00002 is for the 7-transmembrane receptor protein in the secretin family.

tree  = gethmmtree(2, 'type', 'seed')
tree  = gethmmtree('PF00002', 'type', 'seed')

  Phylogenetic tree object with 32 leaves (31 branches)

See Also

gethmmalignment | phytreeread

© 1984-2012- The MathWorks, Inc.    -   Site Help   -   Patents   -   Trademarks   -   Privacy Policy   -   Preventing Piracy   -   RSS