gethgvbase

Extraction of single nucleotide polymorphism data from HGVBASE

Description

%GETHGVBASE returns polymorphism data from the human genome variation db
% http://hgvbase.cgb.ki.se
%
%HGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record from
%EMBL and creates a structure DATA %containing fields corresponding
%to the hgvBase keywords.
%
%FIELDNAME DESCRIPTIONS: a complete %description of field names can be
%found at: %http://hgvbase.cgb.ki.se/cgi-bin/main.pl?page=data_struct.htm
%
% Examples:
%
% data = gethgvbase('SNP000003319')
% hgvData = gethgvbase('SNP000003320')
%
% Reference:
%
%HGVbase: a human sequence variation %database emphasizing data
%quality and a broad spectrum of data %sources. Nucleic Acids Res. 2002 Jan
%1;30(1):387-91.
%
%See also:
%EMBLREAD, FASTAREAD, GENPEPTREAD, %GETGENBANK, SCFREAD, SEQTOOL.
%
%Colin Clarke, Cranfield University - %Analytical Science and Informatics
%$revision 1.0$ $Date: 12/09/2006$
%email: [e-mail]

data = gethgvbase('SNP000003319')

data =

                 snpID: 'SNP000003319'
               varType: 'SNP'
             varStatus: 'Proven'
              geneType: 'Functional Gene'
            geneSymbol: 'COL4A4'
              geneName: 'collagen, type IV, alpha 4'
            geneRegion: 'I-Ex:CDS+'
    downStreamSequence: 'CCAGGACCAGGTATGAGCCGCATGC'
      upStreamSequence: 'TGGGGCTCCCTGGAATGAGAGGCCC'
               alleles: [2x1 char]
              sourceId: [2x12 char]
               DBXREFS: [3x21 char]
              citation: [2x41 char]
               feature: [14x12 char]
           motifChange: []
            population: 'European, African and Middle East (90 individuals)'
                  mesh: [25x31 char]

• MATLAB release: MATLAB 7.2 (R2006a)
• Other requirements: windows and linux compatible