| Bioinformatics Toolbox | |
Retrieve sequence information from EMBL database
Data = getembl('AccessionNumber',
'PropertyName', PropertyValue...)
getembl(..., 'ToFile', ToFileValue)
getembl(..., 'SequenceOnly', SequenceOnlyValue)
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). |
SequenceOnly | Property to control getting a sequence without the metadata. Enter true or false. |
getembl retrieves information from the European Molecular Biology Laboratory (EMBL) database for nucleotide sequences. This database is maintained by the European Bioinformatics Institute (EBI). For more details about the EMBL-Bank database, see
http://www.ebi.ac.uk/embl/Documentation/index.html
Data = getembl('AccessionNumber', 'PropertyName', PropertyValue...) searches for the accession number in the EMBL database (http://www.ebi.ac.uk/embl) and returns a MATLAB structure containing the following fields:
Comments Identification Accession SequenceVersion DateCreated DateUpdated Description Keyword OrganismSpecies OrganismClassification Organelle Reference DatabaseCrossReference Feature BaseCount Sequence
getembl(..., 'ToFile', ToFileValue) returns a structure containing information about the sequence and saves the information in a file using an EMBL data format. If you do not give a location or path to the file, the file is stored in the MATLAB current directory. Read an EMBL formatted file back into MATLAB using the function emblread.
getembl(..., 'SequenceOnly', SequenceOnlyValue) if SequenceOnly is true, returns only the sequence information without the metadata.
Retrieve data for the rat liver apolipoprotein A-I.
emblout = getembl('X00558')
Retrieve data for the rat liver apolipoprotein and save in the file rat_protein. If a filename is given without a path, the file is stored in the current directory.
Seq = getembl('X00558','ToFile','c:\project\rat_protein.txt')
Retrieve only the sequence for the rat liver apolipoprotein.
Seq = getembl('X00558','SequenceOnly',true)
Bioinformatics Toolbox functions emblread, getgenbank, getgenpept, getpdb, getpir
| | getedgesbynodeid (biograph) | getgenbank | |
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