[BioC] BSgenome: dm3 and panTro2

Herve Pages hpages at fhcrc.org
Tue May 27 23:30:24 CEST 2008

Hi Joseph,

Are you sure that the dm3 assembly provided by UCSC (based on BDGP Release 5)
is different from the FlyBase r5.1 assembly? If not then you could just use
the BSgenome.Dmelanogaster.FlyBase.r51 package which contains the FlyBase r5.1
assembly (I think that the differences between the various 5.y releases from
FlyBase are on the annotation side only, but the chromosome sequences should
be the same).

Anyway I've started building a BSgenome package for dm3. Once it's ready it
will be easy to verify that the chromosome sequences are indeed the same than
in FlyBase r5.1 by doing something like:

   r51 <- BSgenome.Dmelanogaster.FlyBase.r51::Dmelanogaster
   dm3 <- BSgenome.Dmelanogaster.UCSC.dm3::Dmelanogaster
   r51$chr2L == unmasked(dm3$chr2L)

I'll take this opportunity to add the same built-in masks to this new package
than the ones I've already added to other BSgenome data packages (only Human,
Mouse and Dog so far). Those built-in masks are new in Bioconductor 2.2 and
some examples on how to use them are shown in the GenomeSearching vignette
(this vignette has been moved from the Biostrings pkg to the BSgenome pkg).

I will also make a BSgenome data pkg for Chimpanzee (with masks too) and post
here again when this is ready.


joseph wrote:
> Hi
> Are there any plans to add the most recent Drosophila and Chimpanzee 
> genomes to the BSgenome list?
> The most recent UCSC versions are the Apr. 2006 assembly of the D. 
> melanogaster genome (dm3) and the Chimpanzee Genome Mar. 2006 
> (panTro2).  The Mac OS packages would be nice to have.
> Thanks
> Joseph

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