This directory contains a dump of the UCSC genome annotation database for the Jul. 2007 Zv7 assembly of the zebrafish genome (danRer5) obtained from the Wellcome Trust Sanger Institute. The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by a collaboration between the Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute for Developmental Biology in Tuebingen, Germany, the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands and Yi Zhou and Leonard Zon from the Children's Hospital in Boston, Massachusetts. For more information on the zebrafish genome, see the project website: http://www.sanger.ac.uk/Projects/D_rerio/ Files included in this directory (updated nightly): - *.sql files: the MySQL commands used to create the tables - *.txt.gz files: the database tables in a tab-delimited format compressed with gzip. To see descriptions of the tables underlying Genome Browser annotation tracks, select the table in the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables?db=danRer5 and click the "describe table schema" button. There is also a "view table schema" link on the configuration page for each track. --------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/danRer5/database/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) Alternate methods to ftp access. Using an rsync command to download the entire directory: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/gc5Base.txt.gz' -O gc5Base.txt.gz To uncompress the *.txt.gz files: gunzip .txt.gz The tables can be loaded directly from the .txt.gz compressed file. It is not necessary to uncompress them to load into a database, as shown in the example below. To load one of the tables directly into your local mirror database, for example the table chromInfo: ## create table from the sql definition $ hgsql danRer5 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql danRer5 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained directly from ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence data are made available before scientific publication with the understanding that the groups involved in generating the data intend to publish the initial large-scale analyses of the dataset. This will include a summary detailing the data that have beeen generated and key features of the genome identified from genomic assembly and clone mapping/sequencing. Any redistribution of the data should carry this notice. All the files and tables in this directory are freely usable for any purpose.