genbankread

Read data from GenBank file

Syntax

GenBankData = genbankread(File)
GenBankData = genbankread(File, 'TimeOut', TimeOutValue)

Arguments

File

Either of the following:

  • Character vector or string specifying a file name, a path and file name, or a URL pointing to a file. The referenced file is a GenBank-formatted file (ASCII text file). If you specify only a file name, that file must be on the MATLAB® search path or in the MATLAB Current Folder.

  • MATLAB character array or string vector that contains the text of a GenBank-formatted file.

Tip

You can use the getgenbank function with the 'ToFile' property to retrieve sequence information from the GenBank® database and create an GenBank-formatted file.

TimeOutValueConnection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.
GenBankData MATLAB structure or array of structures containing fields corresponding to GenBank keywords.

Description

GenBankData = genbankread(File) reads a GenBank-formatted file, File, and creates GenBankData, a structure or array of structures, containing fields corresponding to the GenBank keywords. When File contains multiple entries, each entry is stored as a separate element in GenBankData. For a list of the GenBank keywords, see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html.

GenBankData = genbankread(File, 'TimeOut', TimeOutValue) sets the connection timeout (in seconds) to read data from a remote file or URL.

Examples

  1. Retrieve sequence information for the HEXA gene, store the data in a file, and then read into the MATLAB software.

    getgenbank('nm_000520', 'ToFile', 'TaySachs_Gene.txt')
s = genbankread('TaySachs_Gene.txt')

s = 

                LocusName: 'NM_000520'
      LocusSequenceLength: '2437'
     LocusNumberofStrands: ''
            LocusTopology: 'linear'
        LocusMoleculeType: 'mRNA'
     LocusGenBankDivision: 'PRI'
    LocusModificationDate: '18-FEB-2009'
               Definition: [1x63 char]
                Accession: 'NM_000520'
                  Version: 'NM_000520.4'
                       GI: '189181665'
                  Project: []
                   DBLink: []
                 Keywords: []
                  Segment: []
                   Source: 'Homo sapiens (human)'
           SourceOrganism: [4x65 char]
                Reference: {1x10 cell}
                  Comment: [32x67 char]
                 Features: [147x74 char]
                      CDS: [1x1 struct]
                 Sequence: [1x2437 char]

  2. Display the source organism for this sequence.

    s.SourceOrganism

ans =

Homo sapiens                                                     
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;     
Catarrhini; Hominidae; Homo.

Version History

Introduced before R2006a

See Also

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