Bioinformatics Toolbox™

getembl - Retrieve sequence information from EMBL database

Syntax

EMBLData = getembl(AccessionNumber) EMBLData = getembl(..., 'ToFile', ToFileValue, ...) EMBLSeq = getembl(..., 'SequenceOnly', SequenceOnlyValue, ...)

Arguments

`AccessionNumber`	Unique identifier for a sequence record. Enter a unique combination of letters and numbers.
`ToFileValue`	String specifying a file name or a path and file name to which to save the data. If you specify only a file name, the file is stored in the current directory.
`SequenceOnlyValue`	Controls the retrieving of only the sequence without the metadata. Choices are `true` or `false` (default).

Return Values

`EMBLData`	MATLAB^® structure with fields corresponding to EMBL data.
`EMBLSeq`	MATLAB character string representing the sequence.

Description

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 database, see

http://www.ebi.ac.uk/embl/Documentation/index.html

EMBLData = getembl(AccessionNumber) searches for the accession number in the EMBL database (http://www.ebi.ac.uk/embl) and returns EMBLData, a MATLAB structure with fields corresponding to the EMBL two-character line type code. Each line type code is stored as a separate element in the structure.

EMBLData contains the following fields.

Field
`Identification`
`Accession`
`SequenceVersion`
`DateCreated`
`DateUpdated`
`Description`
`Keyword`
`OrganismSpecies`
`OrganismClassification`
`Organelle`
`Reference`
`DatabaseCrossReference`
`Comments`
`Assembly`
`Feature`
`BaseCount`
`Sequence`

EMBLData = getembl(..., 'PropertyName', PropertyValue, ...) calls getembl with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

EMBLData = getembl(..., 'ToFile', ToFileValue, ...) saves the information to an EMBL-formatted file. ToFileValueis a string specifying a file name or a path and file name to which to save the data. If you specify only a file name, the file is stored in the current directory.

Tip Read an EMBL-formatted file back into the MATLAB software using the emblread function.

EMBLSeq = getembl(..., 'SequenceOnly', SequenceOnlyValue, ...) controls the retrieving of only the sequence without the metadata. Choices are true or false (default).

Examples

Retrieve data for the rat liver apolipoprotein A-I.

emblout = getembl('X00558')

Retrieve data for the rat liver apolipoprotein A-I and save it to the file rat_protein. If you specify a file name without a path, the file is stored in the current directory.

emblout = getembl('X00558','ToFile','c:\project\rat_protein.txt')

Retrieve only the sequence for the rat liver apolipoprotein A-I.