This directory contains a dump of the UCSC genome annotation database for the Jul. 2008 (Broad/choHof1) assembly of the sloth genome (choHof1, Broad Institute choHof1). The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/907 http://www.ncbi.nlm.nih.gov/genome/assembly/199758 http://www.ncbi.nlm.nih.gov/bioproject/30809 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=choHof1 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/choHof1/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/choHof1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/choHof1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/choHof1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/choHof1/database/gc5BaseBw.txt.gz' -O gc5BaseBw.txt.gz Please note that some files contents, such as this example gc5BaseBw.txt.gz, will point to the data being hosted in another /gbdb/ location, which refers to ftp://hgdownload.cse.ucsc.edu/gbdb/ 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 choHof1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql choHof1 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- The Sloth sequence is made freely available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. 3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. 1. The data may be freely downloaded, used in analyses, and repackaged in databases. ----------------------------------------------------------------------------- GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. ----------------------------------------------------------------------------- All the files and tables in this directory are freely usable for any purpose. -----------------------------------------------------------------------------