[BioC] A question about the coordinate system in the yeast database

Hervé Pagès hpages at fhcrc.org
Thu Aug 11 23:12:00 CEST 2011

Hi Xuekui,

On 11-08-08 04:04 PM, Xuekui Zhang wrote:
>   Dear list,
>   I am working with yeast genome "Saccharomyces cerevisiae".
>   My sequences are aligned to reference genome of version "sacCer2".
>   I found the ensembl annotation of genes has 3 versions, including SGD1.01, EF2, and EF3.
> I would like to use same coordinate system for aligned reads and annotated genes.
>   Could anyone explain how to match the two different systems (i.e. sacCer1/sacCer2 vs SGD1/SGD2/EF3)?

Right. Ensembl is currently using the EF3 assembly from February
2011, which is more recent than sacCer2.

Working with two different coord systems sounds tricky and you'll
probably make your life much easier by using the same coord sys
for alignment and annotations. So why not align your sequences to
EF3? Or use annotations from the "Ensembl Genes" track provided
by the UCSC genome browser (for sacCer2) if realigning your
sequences is not an option for you?


> Thanks!
> Xuekui

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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