This directory contains a dump of the UCSC genome annotation database for the Mar. 2011 (Broad/otoGar3) assembly of the bushbaby genome (otoGar3, Broad Institute (GCA_000181295.3)). 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/451 http://www.ncbi.nlm.nih.gov/genome/assembly/249878 http://www.ncbi.nlm.nih.gov/bioproject/16955 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=otoGar3 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/otoGar3/database/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - 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/otoGar3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/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 <table>.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 otoGar3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql otoGar3 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- The Bushbaby 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 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. -----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory - gap.sql 2012-11-21 15:56 1.6K gap.txt.gz 2012-11-21 15:56 2.6M chromInfo.sql 2012-11-21 15:56 1.4K chromInfo.txt.gz 2012-11-21 15:56 33K nestedRepeats.sql 2012-11-21 15:57 1.9K nestedRepeats.txt.gz 2012-11-21 15:57 12M rmsk.sql 2012-11-21 15:57 1.9K rmsk.txt.gz 2012-11-21 15:57 111M simpleRepeat.sql 2012-11-21 15:59 1.9K simpleRepeat.txt.gz 2012-11-21 15:59 13M cpgIslandExt.sql 2012-11-21 15:59 1.7K cpgIslandExt.txt.gz 2012-11-21 15:59 463K netMm10.sql 2012-11-21 15:59 2.1K netMm10.txt.gz 2012-11-21 16:00 59M chainMm10.sql 2012-11-21 16:00 1.7K chainMm10.txt.gz 2012-11-21 16:00 65M windowmaskerSdust.sql 2012-11-21 16:00 1.5K windowmaskerSdust.txt.gz 2012-11-21 16:00 124M chainMm10Link.sql 2012-11-21 16:01 1.5K chainMm10Link.txt.gz 2012-11-21 16:02 480M gold.sql 2012-11-21 16:07 1.7K gold.txt.gz 2012-11-21 16:07 3.3M genscan.sql 2012-11-21 16:07 1.7K genscan.txt.gz 2012-11-21 16:07 3.0M gc5BaseBw.sql 2012-11-21 16:07 1.3K gc5BaseBw.txt.gz 2012-11-21 16:07 63 history.sql 2012-11-21 16:07 1.6K history.txt.gz 2012-11-21 16:07 568 cytoBandIdeo.sql 2013-04-28 19:52 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:52 29K ucscToINSDC.sql 2013-09-15 17:34 1.4K ucscToINSDC.txt.gz 2013-09-15 17:34 49K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 17:53 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:53 482K chainTarSyr2.sql 2015-05-25 06:34 1.7K chainTarSyr2.txt.gz 2015-05-25 06:37 3.0G chainTarSyr2Link.sql 2015-05-25 06:47 1.5K chainTarSyr2Link.txt.gz 2015-05-25 06:57 7.0G netTarSyr2.sql 2015-05-25 07:23 2.1K netTarSyr2.txt.gz 2015-05-25 07:23 64M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.2M microsat.sql 2015-08-23 23:03 1.5K microsat.txt.gz 2015-08-23 23:03 84K all_mrna.sql 2017-07-09 12:08 2.1K all_mrna.txt.gz 2017-07-09 12:08 261 mrnaOrientInfo.sql 2017-07-09 12:09 1.8K mrnaOrientInfo.txt.gz 2017-07-09 12:09 137 chainHg38.sql 2018-01-07 09:47 1.7K chainHg38.txt.gz 2018-01-07 09:47 194M chainHg38Link.sql 2018-01-07 09:48 1.5K chainHg38Link.txt.gz 2018-01-07 09:49 867M netHg38.sql 2018-01-07 09:52 2.1K netHg38.txt.gz 2018-01-07 09:52 60M chromAlias.sql 2018-02-18 07:56 1.4K chromAlias.txt.gz 2018-02-18 07:56 73K ucscToRefSeq.sql 2018-02-18 07:56 1.4K ucscToRefSeq.txt.gz 2018-02-18 07:56 48K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 90 ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 2.5M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 219K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 1.7K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.1M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.2M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.5M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.9M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 577K xenoMrna.sql 2020-08-20 00:12 2.1K xenoMrna.txt.gz 2020-08-20 00:12 448M xenoRefGene.sql 2020-08-20 00:19 2.0K xenoRefGene.txt.gz 2020-08-20 00:19 43M xenoRefFlat.sql 2020-08-20 00:19 1.7K xenoRefFlat.txt.gz 2020-08-20 00:19 39M xenoRefSeqAli.sql 2020-08-20 00:19 2.1K xenoRefSeqAli.txt.gz 2020-08-20 00:19 43M gbLoaded.sql 2020-08-20 00:19 1.6K gbLoaded.txt.gz 2020-08-20 00:19 15K chainMm39.sql 2020-11-24 17:45 1.7K chainMm39.txt.gz 2020-11-24 17:45 49M chainMm39Link.sql 2020-11-24 17:48 1.6K chainMm39Link.txt.gz 2020-11-24 17:48 426M netMm39.sql 2020-11-24 17:51 2.1K netMm39.txt.gz 2020-11-24 17:51 59M ensGene.sql 2021-05-25 14:40 1.9K ensGene.txt.gz 2021-05-25 14:40 2.1M ensGtp.sql 2021-05-25 14:40 1.4K ensGtp.txt.gz 2021-05-25 14:40 278K ensemblToGeneName.sql 2021-05-25 14:40 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:40 142K ensemblSource.sql 2021-05-25 14:41 1.4K ensemblSource.txt.gz 2021-05-25 14:41 86K ensPep.sql 2021-05-25 14:41 1.3K ensPep.txt.gz 2021-05-25 14:41 6.2M trackDb.sql 2024-01-31 15:13 2.1K trackDb.txt.gz 2024-01-31 15:13 45K hgFindSpec.sql 2024-01-31 15:13 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 1.2K tableDescriptions.sql 2024-10-12 02:03 1.5K tableDescriptions.txt.gz 2024-10-12 02:03 6.4K tableList.sql 2024-10-13 03:33 1.6K tableList.txt.gz 2024-10-13 03:33 3.3K bigFiles.sql 2024-10-13 03:33 1.4K bigFiles.txt.gz 2024-10-13 03:33 94