[BioC] question about BSgenome and C.pombe genome, absent in USCS

[Hervé Pagès]

Hi Boris,

On 04/10/2012 01:52 PM, Zybaylov, Boris L wrote:
> Dear list,
>
> I need to find some sequence patterns in C.pombe genome.
>
> I thought to use for it  BSGenome and matchPattern function, however S.pombe is not available in BSgenome.
>
> Is it possible to install C.pombe genome from another source (not USCS) and still use it with BSgenome?

If you are looking for S. pombe (not C. pombe), the sequences of
the 3 chromosomes are available here (as fasta files):

   ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/

Although it would be convenient to wrap the 3 sequences in a BSgenome
data package (and this is pretty easy to do, see the BSgenomeForge
vignette in the BSgenome software package), you don't really need one.
You can just load each sequence individually in your session with
read.DNAStringSet().

Hope this helps.

Cheers,
H.

>
> If not, what are other options?
>
> Thank you!
>
> Best,
>
> Boris
>
>
>
> Dr. Boris Zybaylov
> Instructor
> Department of Biochemistry and Molecular Biology
> University of Arkansas Medical Sciences
> Little Rock, AR
> 1-501-686-7254
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-- 
Hervé Pagès

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