Hello, The details of the assembly are at the bottom of the Yeast sacCer2 gateway page. Click through the "Sequences" link to see the actual list of data.
The data for download using ftp is here: http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/ For the multiz7way, click on the track's name from within the sacCer2 assembly browser for details about the processing, including methods, inputs, and references. We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "kenny daily" <[email protected]> wrote: > From: "kenny daily" <[email protected]> > To: [email protected] > Cc: "Suzanne Sandmeyer" <[email protected]> > Sent: Wednesday, September 9, 2009 2:13:03 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Details about sacCer2 and multiz7way > > Can someone provide more details about the sacCer2 genome and > multiple > alignment multiz7way? How does it match up with the data that is in > SGD, > displayed in their genome browser, etc.? The info site says: > > "The June 2008 (*Saccharomyces cerevisiae*) genome assembly is based > on > sequence dated June 2008 in the Saccharomyces Genome > Database<http://www.yeastgenome.org/>(SGD)." > > Interestingly, nothing in any of the given download directories are > dated > June 2008 - where did this date come from? > > If one looks at SGD's download site ( > http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/) > there are some chromosomes listed at June 2008. However, not all the > chromosomes in the download directory are dated June 2008 - some are > earlier, and some even later. For example: > > chr10.fsa<http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/chr10.fsa>18-Feb-2009 > 15:38 740K > > What is the exact list of chromosome files used to build the sacCer2 > sequence and multiz7way alignment? > > For the other genomes in the multiz7way its easier, as there is a > single, > tar gzipped file for the genome. Is there a way that this type of > download > can be provided for the sacCer2 data? > > Not having exact, replicable instructions for generating and > disseminating > data makes publication and building other tools very difficult. It > would > benefit the community as a whole for some more cooperation between SGD > (or > WormBase, etc.) and the UCSC site, at least so that a user can tell > WHAT > data is being used WHERE and WHEN, three keywords for > reproducibility. > > Thank you very much for any information and assistance. > > -- > Kenny Daily > [email protected] > http://www.kennydaily.net/ > > --- Prediction is very difficult, especially about the future. (Niels > Bohr) > --- > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
