[BioC] comparing multiple individual genomes in bioc?

Kasper Daniel Hansen khansen at stat.berkeley.edu
Tue Jan 27 23:55:51 CET 2009

This is a rather difficult question to answer because no-one has  
really done what you are proposing to do. It is true that many people  
hope to be able to do something like this, but it is unclear how much  
data we are talking about, what form the data is in and finally what  
kind of stuff we want to do with the data. Without a more clear  
specification it is pretty hard to answer this.

There is for example a difference in whether the data is just a list  
of SNPs, a collection of genomes in FASTA format or a (big) collection  
of short reads that needs to be assembled.

Given that no-one has done this, it is clear that the first attempts  
will involve a lot of custom code, so don't expect any off-the-shelf  
method for any suite of software. I will say that Bioconductor is a  
priori not more nor less suitable for this than any other piece of  


On Jan 27, 2009, at 9:21 , Paul Shannon wrote:

> I am becoming acquainted with the bioc packages helpful in DNA  
> sequence analysis.  There is lots of nice stuff.
> We (like the rest of the world...) hope to soon have many individual  
> human genomes.  We wish to compare them, looking for fine-grained  
> variations in intragenic and extragenic regions, for clues to  
> phenotypic variety.
> Is there support for this kind of analysis in bioc?  If not, is this  
> planned or hoped for?
> Thanks -
> - Paul Shannon
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