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Thread Subject:
Turn DNA codon number into base pair number

Subject: Turn DNA codon number into base pair number

From: Sarah

Date: 31 Oct, 2012 17:48:08

Message: 1 of 4

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.

Subject: Turn DNA codon number into base pair number

From: Nasser M. Abbasi

Date: 31 Oct, 2012 19:06:12

Message: 2 of 4

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.

http://www.mathworks.com/help/bioinfo/functionlist.html

--Nasser

Subject: Turn DNA codon number into base pair number

From: Sarah

Date: 1 Nov, 2012 10:38:07

Message: 3 of 4

> You can try checking the Matlab bioinformatic toolbox.
>
> http://www.mathworks.com/help/bioinfo/functionlist.html
>
> --Nasser


Yes I have tried that.

Subject: Turn DNA codon number into base pair number

From: Lucio Cetto

Date: 1 Nov, 2012 14:28:09

Message: 4 of 4

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)
 >> getData(a,'feature','SOD1')

 ans =

     Reference: '21'
         Start: 33031935
          Stop: 33041244
       Feature: 'SOD1'
        Source: 'protein_coding'
         Score: '0.0'
        Strand: '+'
         Frame: '.'
    Attributes: ''

HTH
Lucio

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