Bioinformatics Toolbox™

goannotread - Annotations from Gene Ontology annotated file

Syntax

Annotation = goannotread(File)

Arguments

Description

Annotation = goannotread(File) converts the contents of File, a Gene Ontology annotated file into Annotation, an array of structs. Files should have the structure specified in:

http://www.geneontology.org/GO.annotation.shtml#file

A list with some annotated files can be found at:

http://www.geneontology.org/GO.current.annotations.shtml

Examples

1. Open a Web browser to

   http://www.geneontology.org/GO.current.annotations.shtml

2. Download the file containing GO annotations for the gene products of Saccharomyces cerevisiae (gene_association.sgd.gz) to your MATLAB^® Current Directory.

3. Uncompress the file using the gunzip function.

   gunzip('gene_association.sgd.gz')

4. Read the file into the MATLAB software.

   SGDGenes = goannotread('gene_association.sgd');

5. Create a structure with GO annotations and get a list of genes.

   S = struct2cell(SGDGenes);
   genes = S(3,:)'

See Also

Bioinformatics Toolbox™ functions: geneont (object constructor), num2goid

Bioinformatics Toolbox object: geneont object

Bioinformatics Toolbox methods of geneont object: getancestors, getdescendants, getmatrix, getrelatives

getpdb

gonnet