This directory contains a dump of the UCSC genome annotation database for the Oct. 2010 (BGI CR_1.0/rheMac3) assembly of the rhesus genome (rheMac3, Beijing Genomics Institute, Shenzhen (GCA_000230795.1)). 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/215 http://www.ncbi.nlm.nih.gov/genome/assembly/310688 http://www.ncbi.nlm.nih.gov/bioproject/51409 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=rheMac3 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/rheMac3/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/rheMac3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/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 rheMac3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql rheMac3 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- 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 - chainRn5.sql 2012-11-21 14:34 1.7K chainRn5.txt.gz 2012-11-21 14:34 49M netPonAbe2.sql 2012-11-21 14:34 2.1K netPonAbe2.txt.gz 2012-11-21 14:34 36M all_est.sql 2012-11-21 14:34 2.1K all_est.txt.gz 2012-11-21 14:34 3.5M chainPonAbe2.sql 2012-11-21 14:35 1.7K chainPonAbe2.txt.gz 2012-11-21 14:35 266M chainPonAbe2Link.sql 2012-11-21 14:36 1.6K chainPonAbe2Link.txt.gz 2012-11-21 14:37 817M chainPanTro4Link.sql 2012-11-21 14:42 1.6K chainPanTro4Link.txt.gz 2012-11-21 14:42 165M chainRn5Link.sql 2012-11-21 14:43 1.5K chainRn5Link.txt.gz 2012-11-21 14:43 447M chainMm10.sql 2012-11-21 14:45 1.7K chainMm10.txt.gz 2012-11-21 14:45 60M chainMm10Link.sql 2012-11-21 14:47 1.5K chainMm10Link.txt.gz 2012-11-21 14:48 474M gc5BaseBw.sql 2012-11-21 14:50 1.3K gc5BaseBw.txt.gz 2012-11-21 14:50 63 netPanTro4.sql 2012-11-21 14:50 2.1K netPanTro4.txt.gz 2012-11-21 14:50 28M chainGorGor3Link.sql 2012-11-21 14:50 1.6K chainGorGor3Link.txt.gz 2012-11-21 14:51 646M chainPanTro4.sql 2012-11-21 14:53 1.7K chainPanTro4.txt.gz 2012-11-21 14:53 15M netGorGor3.sql 2012-11-21 14:53 2.1K netGorGor3.txt.gz 2012-11-21 14:53 36M chainCalJac3Link.sql 2012-11-21 14:53 1.6K chainCalJac3Link.txt.gz 2012-11-21 14:53 221M chainGorGor3.sql 2012-11-21 14:54 1.7K chainGorGor3.txt.gz 2012-11-21 14:55 218M gold.sql 2012-11-21 14:55 1.7K gold.txt.gz 2012-11-21 14:55 539K chainMonDom5.sql 2012-11-21 14:55 1.7K chainMonDom5.txt.gz 2012-11-21 14:56 539M gap.sql 2012-11-21 14:58 1.6K gap.txt.gz 2012-11-21 14:58 5.2M netMonDom5.sql 2012-11-21 14:58 2.1K netMonDom5.txt.gz 2012-11-21 14:58 18M chainHg19Link.sql 2012-11-21 14:58 1.5K chainHg19Link.txt.gz 2012-11-21 14:58 168M chainMonDom5Link.sql 2012-11-21 14:59 1.6K ctgPos2.sql 2012-11-21 14:59 1.5K ctgPos2.txt.gz 2012-11-21 14:59 64K chainMonDom5Link.txt.gz 2012-11-21 15:01 1.3G chainHg19.sql 2012-11-21 15:07 1.7K chainHg19.txt.gz 2012-11-21 15:07 15M rmsk.sql 2012-11-21 15:07 1.9K rmsk.txt.gz 2012-11-21 15:07 134M cpgIslandExt.sql 2012-11-21 15:08 1.7K cpgIslandExt.txt.gz 2012-11-21 15:08 546K genscan.sql 2012-11-21 15:08 1.7K genscan.txt.gz 2012-11-21 15:08 2.8M history.sql 2012-11-21 15:08 1.6K history.txt.gz 2012-11-21 15:08 837 estOrientInfo.sql 2012-11-21 15:09 1.8K estOrientInfo.txt.gz 2012-11-21 15:09 776K netCalJac3.sql 2012-11-21 15:09 2.1K netCalJac3.txt.gz 2012-11-21 15:09 46M chainCalJac3.sql 2012-11-21 15:09 1.7K chainCalJac3.txt.gz 2012-11-21 15:09 13M chromInfo.sql 2012-11-21 15:09 1.4K chromInfo.txt.gz 2012-11-21 15:09 118K simpleRepeat.sql 2012-11-21 15:09 1.9K simpleRepeat.txt.gz 2012-11-21 15:09 24M netHg19.sql 2012-11-21 15:10 2.1K netHg19.txt.gz 2012-11-21 15:10 26M nestedRepeats.sql 2012-11-21 15:10 1.9K nestedRepeats.txt.gz 2012-11-21 15:10 17M intronEst.sql 2012-11-21 15:10 2.1K intronEst.txt.gz 2012-11-21 15:10 2.1M netRn5.sql 2012-11-21 15:11 2.1K netRn5.txt.gz 2012-11-21 15:11 70M netMm10.sql 2012-11-21 15:12 2.1K netMm10.txt.gz 2012-11-21 15:12 70M windowmaskerSdust.sql 2012-11-21 15:12 1.5K windowmaskerSdust.txt.gz 2012-11-21 15:12 145M cytoBandIdeo.sql 2013-04-28 21:17 1.5K cytoBandIdeo.txt.gz 2013-04-28 21:17 113K ucscToINSDC.sql 2013-09-15 18:55 1.4K ucscToINSDC.txt.gz 2013-09-15 18:55 188K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 19:17 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:17 1.1M netHg38.sql 2015-05-18 07:55 2.1K netHg38.txt.gz 2015-05-18 07:55 26M chainHg38Link.sql 2015-05-18 07:55 1.5K chainHg38Link.txt.gz 2015-05-18 07:55 176M chainHg38.sql 2015-05-18 07:56 1.7K chainHg38.txt.gz 2015-05-18 07:56 16M chainTarSyr2.sql 2015-05-25 09:10 1.7K chainTarSyr2.txt.gz 2015-05-25 09:10 266M chainTarSyr2Link.sql 2015-05-25 09:11 1.5K chainTarSyr2Link.txt.gz 2015-05-25 09:12 1.1G netTarSyr2.sql 2015-05-25 09:16 2.1K netTarSyr2.txt.gz 2015-05-25 09:16 69M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.1M microsat.sql 2015-08-24 00:53 1.5K microsat.txt.gz 2015-08-24 00:53 262K geneid.sql 2015-11-22 21:02 1.9K geneid.txt.gz 2015-11-22 21:02 2.6M all_mrna.sql 2020-09-01 09:22 2.1K all_mrna.txt.gz 2020-09-01 09:22 16M xenoMrna.sql 2020-09-01 09:22 2.1K xenoMrna.txt.gz 2020-09-01 09:22 323M refGene.sql 2020-09-01 09:22 1.9K refGene.txt.gz 2020-09-01 09:22 571K refFlat.sql 2020-09-01 09:22 1.7K refFlat.txt.gz 2020-09-01 09:22 526K xenoRefGene.sql 2020-09-01 09:22 2.0K xenoRefGene.txt.gz 2020-09-01 09:22 33M xenoRefFlat.sql 2020-09-01 09:22 1.7K xenoRefFlat.txt.gz 2020-09-01 09:22 29M mrnaOrientInfo.sql 2020-09-01 09:22 1.8K mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M refSeqAli.sql 2020-09-01 09:22 2.1K refSeqAli.txt.gz 2020-09-01 09:22 588K xenoRefSeqAli.sql 2020-09-01 09:22 2.1K xenoRefSeqAli.txt.gz 2020-09-01 09:22 34M gbLoaded.sql 2020-09-01 09:22 1.6K gbLoaded.txt.gz 2020-09-01 09:22 81K trackDb.sql 2023-03-28 13:52 2.1K trackDb.txt.gz 2023-03-28 13:52 34K hgFindSpec.sql 2023-03-28 13:52 1.8K hgFindSpec.txt.gz 2023-03-28 13:52 778 tableDescriptions.sql 2024-11-09 02:03 1.5K tableDescriptions.txt.gz 2024-11-09 02:03 5.5K tableList.sql 2024-11-10 03:30 1.6K tableList.txt.gz 2024-11-10 03:30 3.9K bigFiles.sql 2024-11-10 03:30 1.4K bigFiles.txt.gz 2024-11-10 03:30 68