Hi Kenny, The exact details from one of the scientists here below. Jenn ---
The date/time stamps on the download files are: -rw-rw-r-- 1 447313 Jul 31 1996 chr09.fsa -rw-rw-r-- 1 87329 Feb 6 1999 chrmt.fsa -rw-rw-r-- 1 586579 Mar 16 2000 chr05.fsa -rw-rw-r-- 1 274747 Feb 6 2004 chr06.fsa -rw-rw-r-- 1 939935 Feb 27 2004 chr13.fsa -rw-rw-r-- 1 826827 Jul 16 2004 chr02.fsa -rw-rw-r-- 1 963961 Jul 23 2004 chr16.fsa -rw-rw-r-- 1 572119 Nov 8 2005 chr08.fsa -rw-rw-r-- 1 1109574 Jan 6 2006 chr15.fsa -rw-rw-r-- 1 321991 Jan 13 2006 chr03.fsa -rw-rw-r-- 1 1096242 Jan 13 2006 chr12.fsa -rw-rw-r-- 1 797503 Nov 10 2006 chr14.fsa -rw-rw-r-- 1 1109227 Dec 12 2007 chr07.fsa -rw-rw-r-- 1 234140 Mar 5 2008 chr01.fsa -rw-rw-r-- 1 677658 Jun 3 2008 chr11.fsa -rw-rw-r-- 1 758267 Jun 4 2008 chr10.fsa -rw-rw-r-- 1 1557547 Jun 5 2008 chr04.fsa Thus, the last updated sequence from SGD was June 2008 and that is the date we claim on our browser. Their gff feature files update constantly. The timestamps on the files we fetched were: -rw-rw-r-- 1 2586161 Feb 15 2006 scerevisiae_sage.gff -rw-rw-r-- 1 22158 Oct 16 2006 Tachibana2005.gff -rw-rw-r-- 1 663888 Nov 5 2008 SGD_CDS_xref.txt -rw-rw-r-- 1 2688247 Jan 24 2009 SGD_features.tab -rw-rw-r-- 1 4100530 Jan 24 2009 dbxref.tab -rw-rw-r-- 1 278922 Jan 24 2009 genetic_map.tab -rw-rw-r-- 1 32708 Jan 24 2009 clone.tab -rw-rw-r-- 1 291779 Jan 24 2009 annotation_change.tab -rw-rw-r-- 1 334 Jan 24 2009 chromosome_length.tab -rw-rw-r-- 1 18846232 Jan 29 2009 saccharomyces_cerevisiae.gff -rw-rw-r-- 1 567626 Jan 29 2009 scerevisiae_regulatory.gff -rw-rw-r-- 1 201164 Jan 29 2009 scerevisiae_clonedata.gff --Hiram ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "kenny daily" <[email protected]> wrote: > From: "kenny daily" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: "Suzanne Sandmeyer" <[email protected]>, [email protected] > Sent: Wednesday, September 9, 2009 3:18:38 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Details about sacCer2 and multiz7way > > Great, I forgot about those...however, it still doesn't tell me what > was > actually downloaded from SGD... > > On Wed, Sep 9, 2009 at 6:14 PM, Jennifer Jackson <[email protected]> > wrote: > > > 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 > > > > > > -- > 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
