| Bioinformatics Toolbox | |
Retrieve multiple aligned sequences from the PFAM database
AlignData = gethmmalignment('PFAMKey',
'PropertyName', PropertyValue...)
gethmmalignment(..., 'ToFile', ToFileValue)
gethmmalignment(..., 'Type', TypeValue)
PFAMKey | 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). |
Type | Property to select the set of alignments returned. Enter either 'seed' or 'full'. |
AlignData = gethmmalignment('PFAMKey', 'PropertyName',PropertyValue...) retrieves multiple aligned sequences from a profile hidden Markov model stored in the PFAM database and returns a MATLAB structure containing the following fields:
Header Sequence
gethmmalignment(..., 'ToFile', ToFileValue) saves the data returned from the PFAM database to a file. Read a FASTA formatted file with PFAM data back into MATLAB using the function fastaread.
gethmmalignment(..., 'Type', TypeValue) returns only the alignments used to generate the HMM model if Type='seed', and if Type='full', returns all alignments that fit the model. Default is 'full'.
Retrieve a multiple alignment of the sequences used to train the HMM profile model for global alignment to the 7 transmembrane receptor protein in the secretin family (PFAMKey = PF00002).
pfamalign = gethmmalignment(2,'Type','seed')
or
pfamalign = gethmmalignment('PF00002','Type','seed')
Bioinformatics Toolbox function fastaread, gethmmprof, gethmmtree, pfamhmmread
| | getgeodata | gethmmprof | |
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