[BioC] BSgenome package for sacCer3

[Hervé Pagès]

Hi,

This is to announce that a BSgenome package for sacCer3 is now available
in BioC devel (i.e. R 2.14 + BioC 2.9):

 > library(BSgenome.Scerevisiae.UCSC.sacCer2)
 > sacCer2 <- Scerevisiae

 > library(BSgenome.Scerevisiae.UCSC.sacCer3)
 > sacCer3 <- Scerevisiae

 > seqlengths(sacCer2)
    chrI   chrII  chrIII   chrIV    chrV   chrVI  chrVII chrVIII   chrIX 
    chrX
  230208  813178  316617 1531919  576869  270148 1090947  562643  439885 
  745742
   chrXI  chrXII chrXIII  chrXIV   chrXV  chrXVI    chrM 2micron
  666454 1078175  924429  784333 1091289  948062   85779    6318

 > seqlengths(sacCer3)
    chrI   chrII  chrIII   chrIV    chrV   chrVI  chrVII chrVIII   chrIX 
    chrX
  230218  813184  316620 1531933  576874  270161 1090940  562643  439888 
  745751
   chrXI  chrXII chrXIII  chrXIV   chrXV  chrXVI    chrM
  666816 1078177  924431  784333 1091291  948066   85779

The 2micron sequence is gone.

The package is only available as a source package for now. Binaries
for Windows and Mac will follow soon. In the mean time, users on those
platforms should be able to install from source (i.e. with
biocLite(..., type="source")).

Announcement by UCSC:

 
https://lists.soe.ucsc.edu/pipermail/genome-announce/2011-October/000233.html

Starting page for browsing this new assembly:

   http://genome.ucsc.edu/cgi-bin/hgGateway?clade=other&org=S.+cerevisiae

Cheers,
H.

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
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