getembl

Retrieve sequence information from EMBL database

Syntax

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

Input Arguments

`AccessionNumber`	Unique identifier for a sequence record. Enter a unique combination of letters and numbers.
`ToFileValue`	Character vector 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 folder.
`SequenceOnlyValue`	Controls the retrieving of only the sequence without the metadata. Choices are `true` or `false` (default).
`TimeOutValue`	Connection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

Output Arguments

`EMBLData`	MATLAB^® structure with fields corresponding to EMBL data.
`EMBLSeq`	MATLAB character vector 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

https://ena-docs.readthedocs.io/en/latest/retrieval/general-guide.html

EMBLData = getembl(AccessionNumber) searches for the accession number in the EMBL database (https://www.ebi.ac.uk/) 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. ToFileValue is a character vector 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 folder.

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).

EMBLSeq = getembl(..., 'TimeOut', TimeOutValue, ...) sets the connection timeout (in seconds) to retrieve data from EMBL database.

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 folder.

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

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

Seq = getembl('X00558','SequenceOnly',true)

Version History

Introduced before R2006a