Bioinformatics Toolbox™

genbankread - Read data from GenBank^® file

Syntax

GenBankData = genbankread(File)

Arguments

File

Either of the following:

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 Directory.
MATLAB character array that contains the text of a GenBank-formatted file.

GenBankData MATLAB structure with fields corresponding to GenBank keywords.

Description

GenBankData = genbankread(File) reads in a GenBank-formatted file, File, and creates a structure, GenBankData, containing fields corresponding to the GenBank keywords. Each separate sequence listed in the output structure GenBankData is stored as a separate element of the structure.

Examples

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

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

s = 

                LocusName: 'NM_000520'
      LocusSequenceLength: '2255'
     LocusNumberofStrands: ''
            LocusTopology: 'linear'
        LocusMoleculeType: 'mRNA'
     LocusGenBankDivision: 'PRI'
    LocusModificationDate: '13-AUG-2006'
               Definition: [1x63 char]
                Accession: 'NM_000520'
                  Version: 'NM_000520.2'
                       GI: '13128865'
                  Project: []
                 Keywords: []
                  Segment: []
                   Source: 'Homo sapiens (human)'
           SourceOrganism: [4x65 char]
                Reference: {1x58 cell}
                  Comment: [15x67 char]
                 Features: [74x74 char]
                      CDS: [1x1 struct]
                 Sequence: [1x2255 char]

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.

genbankread - Read data from GenBank® file

Syntax

Arguments

Description

Examples

See Also

genbankread - Read data from GenBank^® file