This directory contains a dump of the UCSC genome annotation database for the Jul. 2009 assembly of the elephant genome (loxAfr3, Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)). The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the Broad Institute. For more information on the elephant genome, see the project website: http://www.broadinstitute.org/science/projects/mammals-models/elephant/elephant 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=loxAfr3 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/loxAfr3/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/loxAfr3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/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/ 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/ 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 loxAfr3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql loxAfr3 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G chainHg19Link.txt.gz 2010-03-24 14:06 959M chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M chainMm39Link.txt.gz 2020-11-25 04:21 656M chainMm10Link.txt.gz 2017-04-17 01:54 568M chainMonDom5.txt.gz 2011-11-21 18:25 398M xenoMrna.txt.gz 2020-08-19 13:31 302M chainHg19.txt.gz 2010-03-24 14:02 220M chainNeoSch1.txt.gz 2020-07-15 21:35 198M rmsk.txt.gz 2010-03-24 14:20 148M chainMm10.txt.gz 2013-10-27 17:02 112M chainMm39.txt.gz 2020-11-25 04:15 90M netNeoSch1.txt.gz 2020-07-15 21:44 77M netHg19.txt.gz 2010-03-24 14:22 74M netMm10.txt.gz 2013-10-27 17:05 58M netMm39.txt.gz 2020-11-25 04:23 58M quality.txt.gz 2010-03-24 14:13 55M xenoRefGene.txt.gz 2020-08-19 14:06 36M xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M xenoRefFlat.txt.gz 2020-08-19 14:06 33M netMonDom5.txt.gz 2011-11-21 18:27 19M nestedRepeats.txt.gz 2010-03-24 14:22 17M gc5Base.txt.gz 2010-03-24 14:22 13M simpleRepeat.txt.gz 2010-03-24 14:12 11M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M ensPep.txt.gz 2021-05-25 14:37 7.9M blastHg18KG.txt.gz 2010-03-24 14:21 3.9M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M genscan.txt.gz 2013-12-10 01:52 3.3M ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M geneid.txt.gz 2015-11-22 18:55 2.6M augustusGene.txt.gz 2015-07-26 16:05 2.3M ensGene.txt.gz 2021-05-25 14:35 2.3M gold.txt.gz 2010-03-24 14:13 1.7M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M gap.txt.gz 2010-03-24 14:03 1.3M seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K ensGtp.txt.gz 2021-05-25 14:35 302K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K ensemblToGeneName.txt.gz 2021-05-25 14:35 153K microsat.txt.gz 2015-08-23 20:42 138K ensemblSource.txt.gz 2021-05-25 14:37 86K tRNAs.txt.gz 2012-04-23 04:53 56K trackDb.txt.gz 2023-12-05 13:52 30K chromAlias.txt.gz 2018-08-05 08:02 23K ucscToINSDC.txt.gz 2013-09-15 15:48 19K gbLoaded.txt.gz 2020-08-19 14:06 15K chromInfo.txt.gz 2010-03-24 14:22 13K cytoBandIdeo.txt.gz 2013-04-28 18:08 13K tableDescriptions.txt.gz 2024-11-30 02:03 6.9K tableList.txt.gz 2024-12-01 03:06 3.8K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K netHg19.sql 2010-03-24 14:22 2.3K refSeqAli.txt.gz 2016-09-18 10:07 2.3K blastHg18KG.sql 2010-03-24 14:21 2.3K refGene.txt.gz 2020-08-19 14:02 2.2K xenoRefSeqAli.sql 2020-08-19 14:06 2.1K xenoMrna.sql 2020-08-19 13:31 2.1K netNeoSch1.sql 2020-07-15 21:44 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K netMm39.sql 2020-11-25 04:23 2.1K refSeqAli.sql 2016-09-18 10:07 2.1K all_mrna.sql 2019-07-14 07:57 2.1K netMm10.sql 2013-10-27 17:05 2.1K trackDb.sql 2023-12-05 13:52 2.1K refFlat.txt.gz 2020-08-19 14:02 2.1K all_mrna.txt.gz 2019-07-14 07:57 2.1K simpleRepeat.sql 2010-03-24 14:12 2.0K netMonDom5.sql 2011-11-21 18:27 2.0K nestedRepeats.sql 2010-03-24 14:22 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K rmsk.sql 2010-03-24 14:20 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K xenoRefGene.sql 2020-08-19 14:06 2.0K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K refGene.sql 2020-08-19 14:02 1.9K ensGene.sql 2021-05-25 14:35 1.9K augustusGene.sql 2015-07-26 16:05 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K geneid.sql 2015-11-22 18:55 1.9K quality.sql 2010-03-24 14:12 1.9K gc5Base.sql 2010-03-24 14:22 1.9K mrnaOrientInfo.sql 2019-07-14 07:57 1.8K chainHg19.sql 2010-03-24 14:01 1.8K hgFindSpec.sql 2023-12-05 13:52 1.8K xenoRefFlat.sql 2020-08-19 14:06 1.7K chainNeoSch1.sql 2020-07-15 21:35 1.7K refFlat.sql 2020-08-19 14:02 1.7K chainMm39.sql 2020-11-25 04:15 1.7K gold.sql 2010-03-24 14:13 1.7K chainMm10.sql 2013-10-27 17:02 1.7K tRNAs.sql 2012-04-23 04:53 1.7K genscan.sql 2013-12-10 01:52 1.7K chainMonDom5.sql 2011-11-21 18:23 1.6K gap.sql 2010-03-24 14:03 1.6K gbLoaded.sql 2020-08-19 14:06 1.6K tableList.sql 2024-12-01 03:06 1.6K chainNeoSch1Link.sql 2020-07-15 21:41 1.6K chainMm39Link.sql 2020-11-25 04:21 1.6K history.sql 2010-03-24 14:22 1.6K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K chainMm10Link.sql 2017-04-17 01:46 1.5K chainHg19Link.sql 2010-03-24 14:04 1.5K cytoBandIdeo.sql 2013-04-28 18:08 1.5K microsat.sql 2015-08-23 20:42 1.5K chainMonDom5Link.sql 2011-11-21 18:11 1.5K tableDescriptions.sql 2024-11-30 02:03 1.5K ensGtp.sql 2021-05-25 14:35 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ucscToINSDC.sql 2013-09-15 15:48 1.4K chromAlias.sql 2018-08-05 08:02 1.4K hgFindSpec.txt.gz 2023-12-05 13:52 1.4K ensemblToGeneName.sql 2021-05-25 14:35 1.4K bigFiles.sql 2024-12-01 03:06 1.4K grp.sql 2014-03-02 04:14 1.4K ensemblSource.sql 2021-05-25 14:37 1.4K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ensPep.sql 2021-05-25 14:37 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K chromInfo.sql 2010-03-24 14:22 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K mrnaOrientInfo.txt.gz 2019-07-14 07:57 958 history.txt.gz 2010-03-24 14:22 573 grp.txt.gz 2014-03-02 04:14 208 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 bigFiles.txt.gz 2024-12-01 03:06 73