Finding per gene GC content.

[chadn737]

Does anyone know of a tool to calculate the GC content per gene?

Alternatively if you know where to find the per gene GC content of Arabidopsis, that will work as well.

[Dario1984]

Try installing Repitools for R. Then, have a look at the gcContentCalc function. All you need as parameters is a BSgenome object of the genome sequence of organism you're studying and a GRanges of the gene coordinates.

A list of BSgenome packages for different organisms is listed here. Scroll down until you see all the packages that begin with BSgenome and click on the one you want. For Arabidopsis, the available BSgenome packages are BSgenome.Athaliana.TAIR.04232008 and BSgenome.Athaliana.TAIR.TAIR9

Here's a small example :

> library(Repitools)
> library(BSgenome.Hsapiens.UCSC.hg18)
> genes <- GRanges(c("chr1", "chr2"), IRanges(c(10000, 20000), c(20000, 30000)))
> genes
GRanges with 2 ranges and 0 elementMetadata values:
      seqnames           ranges strand
         <Rle>        <IRanges>  <Rle>
  [1]     chr1 [10000, 20000]      *
  [2]     chr2 [20000, 30000]      *
  ---
  seqlengths:
   chr1 chr2
     NA   NA

> gcContentCalc(genes, Hsapiens)
Calculating GC content.
     <NA>      <NA> 
0.5181482 0.4384562

So, there's 52 % GC in the first gene, and 44 % in the second gene.

[chadn737]

Thanks, exactly what I needed.

[maubp]

For a command line tool, try geecee from EMBOSS

http://emboss.open-bio.org/wiki/Appdoc:Geecee

If you are working in a programming language there is probably a Bio* library that can help. Biopython has an example of calculating the GC of each sequence in a FASTA file and plotting the distribution in its tutorial:

http://biopython.org/DIST/docs/tutorial/Tutorial.html

http://biopython.org/DIST/docs/tutorial/Tutorial.pdf