| Bioinformatics Toolbox | |
Retrieve sequence information from GenPept database
Data = getgenpept('AccessionNumber',
'PropertyName', PropertyValue...)
getgenpept(..., 'ToFile', ToFileValue)
getgenpept(..., 'SequenceOnly', SequenceOnlyValue)
AccessionNumber | Unique identifier for a sequence record. Enter a 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). |
| FileFormat | Property to select the format for the file specified with the property ToFileValue. Enter either 'GenBank' or 'FASTA'. |
SequenceOnly | Property to control getting the sequence only. Enter either true or false. |
getgenpept retrieves a protein (amino acid) sequence and sequence information from the database GenPept. This database is a translation of the nucleotide sequences in GenBank and is maintained by the National Center for Biotechnology Information (NCBI).
Note NCBI has recently changed the name of their protein search engine from GenPept to Entrez Protein. However, the function names in the Bioinformatics Toolbox (getgenpept, genpeptread) are unchanged representing the still-used GenPept report format. |
For more details about the GenBank database, see
http://www.ncbi.nlm.nih.gov/Genbank/
Data = getgenpept('AccessionNumber', 'PropertyName',PropertyValue...) searches for the accession number in the GenPept database and returns a MATLAB structure containing for the sequence. If an error occurs while retrieving the GenBank formatted information, then an attempt is make to retrieve the FASTA formatted data.
getgenpept(..., 'ToFile', ToFileValue) saves the information in a file. If you do not give a location or path to the file, the file is stored in the MATLAB current directory. Read a GenPept formatted file back into MATLAB using the function genpeptread
getgenpept(..., 'FileFormat', FileFormatValue) returns the sequence in the specified format FileFormatValue.
getgenpept(..., 'SequenceOnly', SequenceOnlyValue) returns only the sequence information without the metadata if SequenceOnly is true. When the properties SequenceOnly and ToFile are used together, the output file is in the FASTA format.
getgenpept(...) displays the information to the screen without returning data to a variable. The displayed information includes hyperlinks to the URLs used to search for and retrieve the data.
Retrieve the sequence for the human insulin receptor and store it in structure Seq.
Seq = getgenpept('AAA59174')
Bioinformatics Toolbox functions genpeptread, getembl, getgenbank, getpdb, getpir
| | getgenbank | getgeodata | |
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