| Bioinformatics Toolbox | |
Get phylogenetic tree data from PFAM database
Tree = gethmmtree(AccessionNumber) Tree = gethmmtree(...,'ToFile',ToFileValue) Tree = gethmmtree(...,'Type', TypeValue)
| AccessionNumber | Accession number in the PFAM database |
| ToFile | Property to specify the location and filename for saving data. Enter either a filename or a path and filename supported by your system (ASCII text file). |
| Type | Property to control which alignments are included in the tree. Enter either 'seed' or 'full'. The default value is 'full' |
Tree = gethmmtree(AccessionNumber) searches for the PFAM family accession number in the PFAM database and returns an object (Tree) containing a phylogenetic tree representative of the protein family.
Tree = gethmmtree(...,'ToFile', ToFileValue) saves the data returned from the PFAM database in the file ToFileValue.
Tree = gethmmtree(...,'Type', TypeValue), when Type is 'seed', returns a tree with only the alignments used to generate the HMM model. When Type is 'full', returns a tree with all of the alignments that hit the model. .
Retrieve a phylogenetic tree built 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')
Bioinformatics Toolbox functions, fastaread, gethmmprof, pfamhmmread
| | gethmmprof | getnodesbyid (biograph) | |
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