This directory contains a dump of the UCSC genome annotation database for the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2)) from the Chicken Genome Sequencing Consortium. 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/111 http://www.ncbi.nlm.nih.gov/genome/assembly/317958 http://www.ncbi.nlm.nih.gov/bioproject/13342 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=galGal4 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/galGal4/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/galGal4/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/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 galGal4 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql galGal4 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ------------------------------------------------------------------ The Chicken sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, 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 these data if the providers of these data are properly cited: International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404 See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. Any redistribution of the data should carry this notice. All the files and tables in this directory are freely usable for any purpose. ------------------------------------------------------------------
Name Last modified Size Description
Parent Directory - bigFiles.txt.gz 2024-12-08 03:34 68 bigFiles.sql 2024-12-08 03:34 1.4K tableList.txt.gz 2024-12-08 03:34 4.4K tableList.sql 2024-12-08 03:34 1.6K tableDescriptions.txt.gz 2024-12-07 02:03 7.8K tableDescriptions.sql 2024-12-07 02:03 1.5K hgFindSpec.txt.gz 2024-07-25 09:34 1.1K hgFindSpec.sql 2024-07-25 09:34 1.8K trackDb.txt.gz 2024-07-25 09:34 73K trackDb.sql 2024-07-25 09:34 2.1K gbLoaded.txt.gz 2020-08-21 21:13 44K gbLoaded.sql 2020-08-21 21:13 1.6K xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M xenoRefSeqAli.sql 2020-08-21 20:59 2.1K refSeqAli.txt.gz 2020-08-21 20:58 753K refSeqAli.sql 2020-08-21 20:58 2.1K mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K mrnaOrientInfo.sql 2020-08-21 20:43 1.8K xenoRefFlat.txt.gz 2020-08-21 20:43 20M xenoRefFlat.sql 2020-08-21 20:43 1.7K xenoRefGene.txt.gz 2020-08-21 20:43 22M xenoRefGene.sql 2020-08-21 20:43 2.0K refFlat.txt.gz 2020-08-21 20:38 663K refFlat.sql 2020-08-21 20:38 1.7K refGene.txt.gz 2020-08-21 20:38 711K refGene.sql 2020-08-21 20:38 1.9K xenoMrna.txt.gz 2020-08-21 19:59 173M xenoMrna.sql 2020-08-21 19:59 2.1K all_mrna.txt.gz 2020-08-21 19:59 1.9M all_mrna.sql 2020-08-21 19:59 2.1K all_est.txt.gz 2020-05-08 00:49 36M all_est.sql 2020-05-08 00:49 2.1K intronEst.txt.gz 2020-05-08 00:49 19M intronEst.sql 2020-05-08 00:49 2.1K estOrientInfo.txt.gz 2020-05-08 00:49 7.2M estOrientInfo.sql 2020-05-08 00:49 1.8K ucscToRefSeq.txt.gz 2018-02-18 06:35 132K ucscToRefSeq.sql 2018-02-18 06:35 1.4K chromAlias.txt.gz 2018-02-18 06:35 178K chromAlias.sql 2018-02-18 06:35 1.4K ensGene.txt.gz 2015-09-14 02:15 1.7M ensGene.sql 2015-09-14 02:15 1.9K ensemblToGeneName.txt.gz 2015-09-14 02:15 112K ensemblToGeneName.sql 2015-09-14 02:15 1.4K ensemblSource.txt.gz 2015-09-14 02:15 56K ensemblSource.sql 2015-09-14 02:15 1.4K ensPep.txt.gz 2015-09-14 02:15 5.2M ensPep.sql 2015-09-14 02:15 1.3K ensGtp.txt.gz 2015-09-14 02:14 187K ensGtp.sql 2015-09-14 02:14 1.4K microsat.txt.gz 2015-08-23 17:01 24K microsat.sql 2015-08-23 17:01 1.5K augustusGene.txt.gz 2015-07-26 13:45 1.5M augustusGene.sql 2015-07-26 13:45 1.9K animalQtl.txt.gz 2014-06-29 20:27 33K animalQtl.sql 2014-06-29 20:27 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K netTaeGut2.txt.gz 2014-05-18 18:44 31M netTaeGut2.sql 2014-05-18 18:44 2.1K chainTaeGut2Link.txt.gz 2014-05-18 18:43 222M chainTaeGut2Link.sql 2014-05-18 18:43 1.5K chainTaeGut2.txt.gz 2014-05-18 18:43 18M chainTaeGut2.sql 2014-05-18 18:43 1.7K snp138Seq.txt.gz 2014-03-09 08:45 57M snp138Seq.sql 2014-03-09 08:45 1.3K snp138Mult.txt.gz 2014-03-09 08:45 2.9M snp138Mult.sql 2014-03-09 08:45 2.9K snp138ExceptionDesc.txt.gz 2014-03-09 08:45 1.0K snp138ExceptionDesc.sql 2014-03-09 08:45 1.4K snp138Common.txt.gz 2014-03-09 08:45 383K snp138Common.sql 2014-03-09 08:45 3.0K snp138CodingDbSnp.txt.gz 2014-03-09 08:45 2.3M snp138CodingDbSnp.sql 2014-03-09 08:45 1.7K snp138.txt.gz 2014-03-09 08:44 133M snp138.sql 2014-03-09 08:44 2.9K grp.txt.gz 2014-03-02 03:41 209 grp.sql 2014-03-02 03:41 1.3K pubsBingBlatPsl.txt.gz 2014-01-26 12:58 664K pubsBingBlatPsl.sql 2014-01-26 12:58 2.2K pubsBingBlat.txt.gz 2014-01-26 12:58 844K pubsBingBlat.sql 2014-01-26 12:58 2.4K ucscToINSDC.txt.gz 2013-09-15 13:24 120K ucscToINSDC.sql 2013-09-15 13:24 1.4K ucscToEnsembl.txt.gz 2013-06-16 17:56 99K ucscToEnsembl.sql 2013-06-16 17:56 1.4K cytoBandIdeo.txt.gz 2013-04-28 15:31 79K cytoBandIdeo.sql 2013-04-28 15:31 1.5K netPetMar2.txt.gz 2013-01-24 00:12 2.3M chainPetMar2.txt.gz 2013-01-24 00:12 2.8M chainPetMar2.sql 2013-01-24 00:12 1.7K netPetMar2.sql 2013-01-24 00:12 2.1K chainPetMar2Link.txt.gz 2013-01-24 00:12 12M chainPetMar2Link.sql 2013-01-24 00:12 1.6K chainGeoFor1.txt.gz 2012-08-19 12:04 93M chainGeoFor1.sql 2012-08-19 12:04 1.7K chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M chainGeoFor1Link.sql 2012-08-19 12:01 1.6K netGeoFor1.txt.gz 2012-08-19 12:01 35M netGeoFor1.sql 2012-08-19 12:01 2.1K gc5BaseBw.txt.gz 2012-06-11 07:51 63 gc5BaseBw.sql 2012-06-11 07:51 1.2K chainMm10Link.txt.gz 2012-06-11 07:48 53M chainMm10Link.sql 2012-06-11 07:47 1.5K rmsk.txt.gz 2012-06-11 07:45 14M rmsk.sql 2012-06-11 07:45 1.8K chainMm10.txt.gz 2012-06-11 07:27 7.2M chainMm10.sql 2012-06-11 07:27 1.6K nestedRepeats.txt.gz 2012-06-11 07:25 671K nestedRepeats.sql 2012-06-11 07:25 1.9K gap.txt.gz 2012-06-11 07:11 181K gap.sql 2012-06-11 07:11 1.5K netMm10.txt.gz 2012-06-11 07:09 7.7M netMm10.sql 2012-06-11 07:08 2.0K windowmaskerSdust.txt.gz 2012-06-11 06:59 54M windowmaskerSdust.sql 2012-06-11 06:58 1.4K cpgIslandExt.txt.gz 2012-06-11 06:23 472K cpgIslandExt.sql 2012-06-11 06:23 1.6K simpleRepeat.txt.gz 2012-06-11 06:21 4.9M simpleRepeat.sql 2012-06-11 06:21 1.9K chromInfo.txt.gz 2012-06-11 06:21 78K chromInfo.sql 2012-06-11 06:21 1.3K genscanSubopt.txt.gz 2012-06-11 06:21 2.8M genscanSubopt.sql 2012-06-11 06:20 1.5K gold.txt.gz 2012-06-11 06:20 213K gold.sql 2012-06-11 06:20 1.6K genscan.txt.gz 2012-06-11 06:20 1.4M genscan.sql 2012-06-11 06:20 1.6K history.txt.gz 2012-06-11 06:20 392 history.sql 2012-06-11 06:20 1.5K