| Bioinformatics Toolbox | |
Retrieve profile hidden Markov models from the PFAM database
Model = gethmmprof('AccessionNumber',
'PropertyName', PropertyValue...)
gethmmprof(..., 'ToFile', ToFileValue)
gethmmprof(..., 'Mode', ModeValue)
AccessionNumber | Unique identifier for a sequence record. Enter a unique combination of letters and numbers. |
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). |
Mode | Property to select returning the global or local alignment mode. Enter either 'ls' for the global alignment mode or 'fs' for the local alignment mode. Default value is 'ls'. |
Model = gethmmprof('AccessionNumber', 'PropertyName',PropertyValue...) searches for the PFAM family accession number in the PFAM database and returns a MATLAB structure containing the following fields:
Name PfamAccessionNumber ModelDescription ModelLength Alphabet MatchEmission InsertEmission NullEmission BeginX MatchX InsertX DeleteX FlankingInsertX
gethmmprof(..., 'ToFile', ToFileValue) saves data returned from the PFAM database in a file (ToFileValue). Read a hmmprof formatted file back into MATLAB using the function pfamhmmread.
gethmmprof(..., 'Mode', ModeValue) selects either the global alignment model or the local alignment model.
Retrieve a HMM profile model for global alignment to the 7 transmembrane receptor protine in the secretin family. (PFAM key = PF00002)
hmmmodel = gethmmprof(2)
or
hmmmodel = gethmmprof('PF00002')
Bioinformatics Toolbox functions hmmprofalign, hmmprofstruct, pfamhmmread, showhmmprof
| | gethmmalignment | gethmmtree | |
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