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
