[BiO BB] GC variation in Genome

Thomas Sicheritz-Ponten thomas at cbs.dtu.dk
Tue Oct 14 06:46:43 EDT 2003

Short answers:

for visualisation of GC content etc.: 
    Artemis: http://www.sanger.ac.uk/Software/Artemis/
    Genome Atlas: http://www.cbs.dtu.dk/services/GenomeAtlas/

for a phylogenomic analysis, mining possible HGT's: 
    PyPhy http://www.cbs.dtu.dk/staff/thomas/pyphy/


Adarsh Ramakumar <adarshramakumar at yahoo.co.uk> writes:

> Dear all,
> A warm hello!  Based on you expertice, I was
> interested to ask you guys for some opinions and I
> would highly appreciate if you could sqeeze in any
> time you have for me to reply.
> Basically I am working with a very peculiar
> prokaryotic genome(yet to be annotated) and I am sure
> you agree with me that they are all unique in their
> own ways. 
> I am confronted with a few difficulties and felt I
> could run by you to have your opinion on it.
> There is a very high GC variation(as low as 40-67% at
> some regions) in the so far highly polished genome
> contig we have. I believe and suspect a lot of lateral
> gene transfers and funny starts and codon usage
> statistics. I would like to basically understand these
> variation and quantify them with respect to their
> inherent nature of variation.
> I am looking at finding these regions of variations,
> first of all to see if they(these variation in
> geneome) are close to each other in clusters or
> entirely in random at different regions of genome,
> then I would like to see the gene's in these regions
> and study their codon usage(if they are similar or
> different and how variable are these with amongst
> themselves), extract such typical funny ones,
> statistically group them according to their location
> in genome, and then try to do some similarity searches
> to fish out if any homologs from other published data,
> try to build a phyologenitc tree to derive at
> conclusion of variation, gene families and so on.
> Could you guys suggest how I could do them or rather
> best way of doing it? I mean is there any software
> that you know off where I can graphically see the
> variations in the contigs with respect to GC?
> I would be very grateful and highly appreciate of any
> time you can offer to inform me on these issues.
> Hoping to hear soon. Have a great day!
> Thanks and Regards

Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org      (
Center for Biological Sequence Analysis		          \
BioCentrum-DTU, Technical University of Denmark            )
CBS: +45 45 252485      Building 208, DK-2800 Lyngby  ##----->
Fax: +45 45 931585      http://www.cbs.dtu.dk/thomas       )
     ... damn arrow eating trees ...                     (

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