In article <nakai-1508961119460001 at 133.1.132.91>,
Kenta Nakai <nakai at imcb.osaka-u.ac.jp> wrote:
>I want to have the latest set of yeast peptide sequences
>locally. I dowloaded the nucleotide sequences from
>genome-ftp.stanford.edu and their annotations from MIPS.
>However, these data were not synchronized. For example,
>according to the current annotation, the length of chr I
>is 230209 nt. (Aug.14) but the chr I sequence stored at
>Stanford U. is 230196 nt. Since the Internet link between
>MIPS and Japan is not thick, it is a rather difficult task to
>download the uncompressed sequence data from MIPS. Aren't
>the genomic sequence data mirrored at Stanford or Japan?
>Any advices or comments are welcome.
>>Kenta Nakai, Ph. D
>Institute for Molecular and Cellular Biology
>Osaka University
>nakai at imcb.osaka-u.ac.jp
There is no automatic mirroring between MIPS and SGD, and I do not
know of any mirrors of either site in Japan. The only mirror of the
SGD ftp site that I am aware of is in Switzerland at the European
Center for Biotechnology Information (ftp.ecbi.org).
Chromosome I is a good example of why there is no automatic mirroring.
Neither MIPS or SGD are the source for chromosome I, Dr. Bussey's
group in Canada is the author of this chromosome's sequence. At SGD
we prefer to only include sequences that have been submitted to
GenBank/EMBL/DDBJ. Once we identify a new sequence we process it for
integration into our database. I am sorry that we are currently a
little behind in this work I hope we will be fully staffed again soon.
However the chromosome I sequence was updated in SGD yesterday.
ftp://genome-ftp/yeast/genome_seq/
I should also note that if you retrieve the sequence from SGD you can
also retrieve tables of ORF locations too. Look in the
yeast/tables/ORF_Locations/ directory. You can also retrieve the
sequence of any arbitrary region of the yeast genome, or the ORFs in
those regions through the SGD WWW pages. See the table at:
http://genome-www.stanford.edu/Saccharomyces/chromosomes.html
There will certainly be minor differences between the information at
MIPS and at SGD. Each site has a slightly different focus and method
of annotation.
Mike
Address for the Saccharomyces Genome Database (SGD) Project
e-mail: yeast-curator at genome.stanford.edu
Telephone: 415-725-8956
ftp: genome-ftp.stanford.edu
WWW: http://genome-www.stanford.edu/
FAX: 415-723-7016
