[BiO BB] GC content

Seema Trivedi svtrived at hotmail.com
Thu Mar 11 09:21:39 EST 2010


If you are looking for CG content of the genomes, you can try NCBI complete genome page. The complete genome page browsing will take you to the genome project pages (at times or else the statistics of the genome). This is where you can get the total no. of genes, total no. of protein coding genes, RNA coding genes etc. besides the CG content of the genome. Moreover, there are no. of software that can help you calculate CG content of a sequence. I can try relocating the names of those in case NCBI is not of help (which I am sure will provide information that you need). Else you can write a small perl script to do it for you.

S Trivedi

> Date: Tue, 9 Mar 2010 13:39:58 +1300
> From: naveejoshi at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] GC content
> Hi Kiekyon
> For obtaining any information about the fungal genes and protein you
> can refer to the Saccharomyces Genome Database(SGD). If you are not able to
> find the specific information its always advisable to ask the curators. I am
> working on the evolution of yeast genes and I also did the same thing when I
> could not find the information I was looking for. They sent me few links
> which really helped me a lot.
> Hope it helps you too.
> On Mon, Mar 8, 2010 at 11:53 PM, <kiekyon.huang at gmail.com> wrote:
> > Hi all,
> >
> > I am looking for materials on the genomic GC content in fungi. Does anybody
> > know of such resources?
> > I had a fungal genome with a genomic GC content of 60%, 60.7% in the coding
> > region, and 58% in the non-coding. Need to compare this with other related
> > fungi. Also, I would like to know what analysis would be more meaningful in
> > this aspect. CpG island or just CpG dinucleotide?
> >
> > thanks a lot!
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> >
> -- 
> Regards,
> Naveen Joshi
> Undergraduate Intern,
> Computational Evolution Group,
> University of Auckland,
> New Zealand
> 00642102249099
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