On 10/31/2012 12:48 PM, Sarah wrote:
> I have many codon numbers for various genes including SOD1, FUS, OPTN etc and I want to know the location in terms of base pair number.
> example: the start codon of the SOD1 gene on chromosome 21 is at base pair number: 33,032,083.
You can try checking the Matlab bioinformatic toolbox.
You can download from ENSEMBL a tab-separated-value table will all the genes (similarly to what the example RNASEQDEDEMO explains, type in the MATLAB command window "showdemo rnaseqdedemo", you must have 12b or later). Then use the provided helper function (ensemblmart2gff) to convert this table to a GFF file and load it into MATLAB as follows:
>> GFFfilename = ensemblmart2gff('ensemblmart_genes_hum37.txt');
>> a = GFFAnnotation(GFFfilename)