Getting Sequence Information from a Public Database :: Sequence Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Getting Sequence Information from a Public Database

Many public databases for nucleotide sequences (for example, GenBank, EMBL-EBI) are accessible from the Web. The MATLAB Command Window with the MATLAB Help browser provide an integrated environment for searching the Web and bringing sequence information into MATLAB.

After you locate a sequence, you need to move the sequence data into the MATLAB workspace.

Open the MATLAB Help browser to the NCBI web site. In the MATLAB Command Window, type
```
web('http://www.ncbi.nlm.nih.gov/')
```
The MATLAB Help browser window opens with the NCBI home page.
Search for the gene you are interested in studying. For example, from the Search list, select Nucleotide, and in the for box enter Tay-Sachs.

The search returns entries for the genes that code the alpha and beta subunits of the enzyme hexosaminidase A (Hex A), and the gene that codes the activator enzyme. The NCBI reference for the human gene HEXA has accession number NM_000520.

Get sequence data into MATLAB. For example, to get sequence information for the human gene HEXA, type

humanHEXA = getgenbank('NM_000520')

Note that blank spaces in GenBank accession numbers use the underline character. Entering 'NM 00520' returns the wrong entry.

The human gene is loaded into the MATLAB workspace as a structure.

humanHEXA = 
                LocusName: 'HEXA'
      LocusSequenceLength: '2255'
     LocusNumberofStrands: ''
            LocusTopology: 'linear'
        LocusMoleculeType: 'mRNA'
     LocusGenBankDivision: 'PRI'
    LocusModificationDate: '10-MAY-2002'
               Definition: [1x63 char]
                Accession: 'NM_000520'
                  Version: '     NM_000520.2'
                       GI: '13128865'
                 Keywords: '.'
                  Segment: []
                   Source: [1x87 char]
           SourceOrganism: [2x65 char]
                Reference: {1x7 cell}
                  Comment: [15x67 char]
                 Features: [71x79 char]
                BaseCount: [1x1 struct]
                 Sequence: [1x2255 char]

Finding a Model Organism to Study

Searching a Public Database for Related Genes