genbankread - Read data from GenBank file

Syntax

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 Folder. MATLAB character array 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.

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 http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html.

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.

See Also

emblread | fastaread | genpeptread | getgenbank | scfread | seqtool

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