This directory contains a dump of the UCSC genome annotation database for the Mar. 2012 (Baylor Panu_2.0/papAnu2) assembly of the baboon genome (papAnu2, Baylor College of Medicine). 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/394 http://www.ncbi.nlm.nih.gov/genome/assembly/383538 http://www.ncbi.nlm.nih.gov/bioproject/54005 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=papAnu2 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/papAnu2/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/papAnu2/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/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 papAnu2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql papAnu2 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' For conditions of use regarding the Baboon genome sequence data, see http://www.hgsc.bcm.edu/content/conditions-use ----------------------------------------------------------------------------- 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 - gc5BaseBw.txt.gz 2013-01-22 13:01 63 ncbiRefSeqOther.txt.gz 2018-08-14 02:21 75 extNcbiRefSeq.txt.gz 2018-08-14 02:21 90 bigFiles.txt.gz 2024-10-06 03:37 94 grp.txt.gz 2014-03-02 04:14 208 history.txt.gz 2013-01-22 13:01 375 hgFindSpec.txt.gz 2023-12-05 13:51 1.2K gc5BaseBw.sql 2013-01-22 13:01 1.3K ncbiRefSeqOther.sql 2018-08-14 02:21 1.3K ensPep.sql 2018-02-04 08:54 1.3K grp.sql 2014-03-02 04:14 1.3K ensemblSource.sql 2018-02-04 08:56 1.4K ucscToEnsembl.sql 2015-04-13 05:01 1.4K ncbiRefSeqCds.sql 2018-08-14 02:21 1.4K ncbiRefSeqPepTable.sql 2018-08-14 02:21 1.4K chromInfo.sql 2013-01-22 13:02 1.4K ensemblToGeneName.sql 2018-02-04 08:57 1.4K bigFiles.sql 2024-10-06 03:37 1.4K ensGtp.sql 2018-02-04 08:54 1.4K chromAlias.sql 2018-02-18 08:15 1.4K ucscToRefSeq.sql 2018-02-18 08:15 1.4K tableDescriptions.sql 2024-10-05 02:03 1.5K extNcbiRefSeq.sql 2018-08-14 02:21 1.5K microsat.sql 2015-08-24 00:04 1.5K windowmaskerSdust.sql 2013-01-22 13:00 1.5K cytoBandIdeo.sql 2013-04-28 20:39 1.5K chainTarSyr2Link.sql 2015-05-25 08:16 1.5K genscanSubopt.sql 2013-01-22 13:01 1.6K seqNcbiRefSeq.sql 2018-08-14 02:21 1.6K history.sql 2013-01-22 13:01 1.6K tableList.sql 2024-10-06 03:37 1.6K gap.sql 2013-01-22 13:04 1.6K gbLoaded.sql 2020-08-22 22:18 1.6K gold.sql 2013-01-22 13:02 1.7K genscan.sql 2013-01-22 13:01 1.7K cpgIslandExt.sql 2013-01-22 12:58 1.7K chainTarSyr2.sql 2015-05-25 08:21 1.7K cpgIslandExtUnmasked.sql 2014-06-01 18:39 1.7K refFlat.sql 2020-08-22 22:18 1.7K xenoRefFlat.sql 2020-08-22 22:18 1.7K hgFindSpec.sql 2023-12-05 13:51 1.8K estOrientInfo.sql 2016-07-10 09:15 1.8K mrnaOrientInfo.sql 2020-05-08 21:41 1.8K rmsk.sql 2013-01-22 12:58 1.9K geneid.sql 2015-11-22 20:32 1.9K ensGene.sql 2018-02-04 08:56 1.9K simpleRepeat.sql 2013-01-22 12:58 1.9K nestedRepeats.sql 2013-01-22 12:58 1.9K augustusGene.sql 2015-07-26 17:21 1.9K refGene.sql 2020-08-22 22:18 1.9K ncbiRefSeq.sql 2018-02-09 13:46 2.0K xenoRefGene.sql 2020-08-22 22:18 2.0K ncbiRefSeqCurated.sql 2018-02-09 13:46 2.0K ncbiRefSeqPredicted.sql 2018-02-09 13:46 2.0K ncbiRefSeqLink.sql 2018-02-09 13:46 2.0K trackDb.sql 2023-12-05 13:51 2.1K netTarSyr2.sql 2015-05-25 08:21 2.1K all_est.sql 2016-07-10 09:15 2.1K all_mrna.sql 2020-03-01 08:34 2.1K intronEst.sql 2016-07-10 09:15 2.1K xenoMrna.sql 2020-08-22 21:58 2.1K refSeqAli.sql 2020-05-08 21:41 2.1K ncbiRefSeqPsl.sql 2018-02-09 13:46 2.1K xenoRefSeqAli.sql 2020-08-22 22:18 2.1K tableList.txt.gz 2024-10-06 03:37 3.3K tableDescriptions.txt.gz 2024-10-05 02:03 6.3K mrnaOrientInfo.txt.gz 2020-05-08 21:41 17K trackDb.txt.gz 2023-12-05 13:51 31K ncbiRefSeqCurated.txt.gz 2018-02-09 13:46 38K all_mrna.txt.gz 2020-03-01 08:34 38K gbLoaded.txt.gz 2020-08-22 22:18 41K refFlat.txt.gz 2020-08-22 22:18 41K refGene.txt.gz 2020-08-22 22:18 45K refSeqAli.txt.gz 2020-05-08 21:41 47K ensemblSource.txt.gz 2018-02-04 08:56 93K ensemblToGeneName.txt.gz 2018-02-04 08:57 156K ncbiRefSeqCds.txt.gz 2018-08-14 02:21 194K ucscToEnsembl.txt.gz 2015-04-13 05:01 299K chromInfo.txt.gz 2013-01-22 13:02 300K ensGtp.txt.gz 2018-02-04 08:54 302K cytoBandIdeo.txt.gz 2013-04-28 20:39 308K microsat.txt.gz 2015-08-24 00:04 314K ucscToRefSeq.txt.gz 2018-02-18 08:15 454K seqNcbiRefSeq.txt.gz 2018-08-14 02:21 504K cpgIslandExt.txt.gz 2013-01-22 12:58 597K chromAlias.txt.gz 2018-02-18 08:15 615K ncbiRefSeqLink.txt.gz 2018-02-09 13:46 964K gold.txt.gz 2013-01-22 13:02 1.0M estOrientInfo.txt.gz 2016-07-10 09:15 1.7M cpgIslandExtUnmasked.txt.gz 2014-06-01 18:39 1.7M gap.txt.gz 2013-01-22 13:04 1.7M augustusGene.txt.gz 2015-07-26 17:21 1.9M geneid.txt.gz 2015-11-22 20:32 2.1M ensGene.txt.gz 2018-02-04 08:56 2.3M ncbiRefSeqPredicted.txt.gz 2018-02-09 13:46 2.5M ncbiRefSeq.txt.gz 2018-02-09 13:46 2.5M genscan.txt.gz 2013-01-22 13:01 2.5M ncbiRefSeqPsl.txt.gz 2018-02-09 13:46 2.8M intronEst.txt.gz 2016-07-10 09:15 3.1M genscanSubopt.txt.gz 2013-01-22 13:01 5.9M all_est.txt.gz 2016-07-10 09:15 6.2M ncbiRefSeqPepTable.txt.gz 2018-08-14 02:21 6.4M ensPep.txt.gz 2018-02-04 08:54 6.4M nestedRepeats.txt.gz 2013-01-22 12:58 18M simpleRepeat.txt.gz 2013-01-22 12:58 29M xenoRefFlat.txt.gz 2020-08-22 22:18 33M xenoRefSeqAli.txt.gz 2020-08-22 22:18 35M xenoRefGene.txt.gz 2020-08-22 22:18 36M netTarSyr2.txt.gz 2015-05-25 08:21 71M chainTarSyr2.txt.gz 2015-05-25 08:21 129M rmsk.txt.gz 2013-01-22 12:58 137M windowmaskerSdust.txt.gz 2013-01-22 13:00 144M xenoMrna.txt.gz 2020-08-22 21:58 344M chainTarSyr2Link.txt.gz 2015-05-25 08:18 832M