This directory contains a dump of the UCSC genome annotation database for the Jul. 2013 (C_griseus_v1.0/criGri1) assembly of the chinese hamster genome (criGri1, Beijing Genomics Institution-Shenzhen) . 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/2791 http://www.ncbi.nlm.nih.gov/genome/assembly/40911 http://www.ncbi.nlm.nih.gov/bioproject/167053 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=criGri1 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/criGri1/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/criGri1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/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 criGri1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql criGri1 --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 - chainCriGriChoV1Link.txt.gz 2017-11-26 06:25 3.5G chainHg19Link.txt.gz 2014-05-08 11:59 1.0G chainCriGriChoV1.txt.gz 2017-11-26 06:18 788M chainHg19.txt.gz 2014-05-08 11:56 266M rmsk.txt.gz 2014-05-08 12:03 101M windowmaskerSdust.txt.gz 2014-05-08 12:04 84M netHg19.txt.gz 2014-05-08 12:02 51M xenoRefSeqAli.txt.gz 2020-08-18 20:53 44M xenoRefGene.txt.gz 2020-08-18 20:40 42M xenoRefFlat.txt.gz 2020-08-18 20:53 38M simpleRepeat.txt.gz 2014-05-08 12:03 23M netCriGriChoV1.txt.gz 2017-11-26 06:38 16M locusName.txt.gz 2017-08-20 09:02 9.1M nestedRepeats.txt.gz 2014-05-08 11:57 8.9M genscan.txt.gz 2014-05-08 12:03 3.0M gold.txt.gz 2014-05-08 12:03 3.0M all_mrna.txt.gz 2018-11-04 06:14 2.9M crisprRanges.txt.gz 2017-08-20 09:02 2.1M augustusGene.txt.gz 2015-07-26 11:46 2.1M gap.txt.gz 2014-05-08 12:03 2.0M microsat.txt.gz 2015-08-23 12:50 2.0M mrnaOrientInfo.txt.gz 2020-05-06 06:16 802K cpgIslandExtUnmasked.txt.gz 2014-05-08 12:03 309K ucscToINSDC.txt.gz 2014-05-08 12:03 307K cpgIslandExt.txt.gz 2014-05-08 12:03 290K chromInfo.txt.gz 2014-05-08 12:02 200K cytoBandIdeo.txt.gz 2014-05-08 12:03 185K gbLoaded.txt.gz 2020-08-18 20:53 65K refSeqAli.txt.gz 2020-05-06 06:20 44K trackDb.txt.gz 2023-03-28 13:47 39K refGene.txt.gz 2020-08-18 20:36 39K refFlat.txt.gz 2020-08-18 20:36 36K tableDescriptions.txt.gz 2024-12-07 02:03 5.3K tableList.txt.gz 2024-12-08 03:29 2.7K xenoRefSeqAli.sql 2020-08-18 20:53 2.1K refSeqAli.sql 2020-05-06 06:20 2.1K netCriGriChoV1.sql 2017-11-26 06:38 2.1K intronEst.sql 2014-05-08 11:56 2.1K xenoMrna.sql 2018-07-29 05:38 2.1K all_mrna.sql 2018-11-04 06:14 2.1K all_est.sql 2014-05-08 11:56 2.1K netHg19.sql 2014-05-08 12:02 2.1K trackDb.sql 2023-03-28 13:47 2.1K xenoRefGene.sql 2020-08-18 20:40 2.0K refGene.sql 2020-08-18 20:36 1.9K augustusGene.sql 2015-07-26 11:46 1.9K nestedRepeats.sql 2014-05-08 11:57 1.9K simpleRepeat.sql 2014-05-08 12:03 1.9K rmsk.sql 2014-05-08 12:03 1.9K mrnaOrientInfo.sql 2020-05-06 06:16 1.8K estOrientInfo.sql 2014-05-08 12:03 1.8K hgFindSpec.sql 2023-03-28 13:47 1.8K xenoRefFlat.sql 2020-08-18 20:53 1.7K refFlat.sql 2020-08-18 20:36 1.7K chainCriGriChoV1.sql 2017-11-26 06:17 1.7K cpgIslandExtUnmasked.sql 2014-05-08 12:03 1.7K chainHg19.sql 2014-05-08 11:56 1.7K cpgIslandExt.sql 2014-05-08 12:03 1.7K genscan.sql 2014-05-08 12:03 1.7K gold.sql 2014-05-08 12:03 1.7K gbLoaded.sql 2020-08-18 20:53 1.6K gap.sql 2014-05-08 12:03 1.6K history.sql 2014-05-08 12:03 1.6K tableList.sql 2024-12-08 03:29 1.6K chainCriGriChoV1Link.sql 2017-11-26 06:20 1.6K chainHg19Link.sql 2014-05-08 11:57 1.5K cytoBandIdeo.sql 2014-05-08 12:03 1.5K locusName.sql 2017-08-20 09:02 1.5K microsat.sql 2015-08-23 12:50 1.5K windowmaskerSdust.sql 2014-05-08 12:03 1.5K crisprRanges.sql 2017-08-20 09:02 1.4K tableDescriptions.sql 2024-12-07 02:03 1.4K ucscToINSDC.sql 2014-05-08 12:03 1.4K chromInfo.sql 2014-05-08 12:02 1.4K bigFiles.sql 2024-12-08 03:29 1.4K grp.sql 2014-05-08 12:03 1.3K crisprTargets.sql 2017-08-20 09:02 1.3K gc5BaseBw.sql 2014-05-08 12:03 1.3K all_est.txt.gz 2014-05-08 11:56 790 hgFindSpec.txt.gz 2023-03-28 13:47 697 intronEst.txt.gz 2014-05-08 11:56 533 history.txt.gz 2014-05-08 12:03 466 estOrientInfo.txt.gz 2014-05-08 12:03 278 grp.txt.gz 2014-05-08 12:03 206 bigFiles.txt.gz 2024-12-08 03:29 92 gc5BaseBw.txt.gz 2014-05-08 12:03 66 crisprTargets.txt.gz 2017-08-20 09:02 61 xenoMrna.txt.gz 2018-07-29 05:38 33