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 - xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M xenoRefSeqAli.sql 2020-08-19 14:06 2.1K xenoRefGene.txt.gz 2020-08-19 14:06 36M xenoRefGene.sql 2020-08-19 14:06 1.9K xenoRefFlat.txt.gz 2020-08-19 14:06 33M xenoRefFlat.sql 2020-08-19 14:06 1.7K xenoMrna.txt.gz 2020-08-19 13:31 302M xenoMrna.sql 2020-08-19 13:31 2.1K ucscToINSDC.txt.gz 2013-09-15 15:48 19K ucscToINSDC.sql 2013-09-15 15:48 1.4K trackDb.txt.gz 2021-12-27 12:23 41K trackDb.sql 2021-12-27 12:23 2.1K tableList.txt.gz 2022-08-07 03:03 3.8K tableList.sql 2022-08-07 03:03 1.6K tableDescriptions.txt.gz 2021-03-13 06:37 6.7K tableDescriptions.sql 2021-03-13 06:37 1.4K tRNAs.txt.gz 2012-04-23 04:53 56K tRNAs.sql 2012-04-23 04:53 1.7K simpleRepeat.txt.gz 2010-03-24 14:12 11M simpleRepeat.sql 2010-03-24 14:12 2.0K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K rmsk.txt.gz 2010-03-24 14:20 148M rmsk.sql 2010-03-24 14:20 2.0K refSeqAli.txt.gz 2016-09-18 10:07 2.3K refSeqAli.sql 2016-09-18 10:07 2.1K refGene.txt.gz 2020-08-19 14:02 2.2K refGene.sql 2020-08-19 14:02 1.9K refFlat.txt.gz 2020-08-19 14:02 2.1K refFlat.sql 2020-08-19 14:02 1.7K quality.txt.gz 2010-03-24 14:13 55M quality.sql 2010-03-24 14:12 1.9K netNeoSch1.txt.gz 2020-07-15 21:44 77M netNeoSch1.sql 2020-07-15 21:44 2.1K netMonDom5.txt.gz 2011-11-21 18:27 19M netMonDom5.sql 2011-11-21 18:27 2.0K netMm39.txt.gz 2020-11-25 04:23 58M netMm39.sql 2020-11-25 04:23 2.1K netMm10.txt.gz 2013-10-27 17:05 58M netMm10.sql 2013-10-27 17:05 2.1K netHg19.txt.gz 2010-03-24 14:22 74M netHg19.sql 2010-03-24 14:22 2.3K nestedRepeats.txt.gz 2010-03-24 14:22 17M nestedRepeats.sql 2010-03-24 14:22 2.0K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M ncbiRefSeq.sql 2020-05-10 03:28 1.9K mrnaOrientInfo.txt.gz 2019-07-14 07:57 958 mrnaOrientInfo.sql 2019-07-14 07:57 1.8K microsat.txt.gz 2015-08-23 20:42 138K microsat.sql 2015-08-23 20:42 1.5K history.txt.gz 2010-03-24 14:22 573 history.sql 2010-03-24 14:22 1.6K hgFindSpec.txt.gz 2021-12-27 12:23 1.3K hgFindSpec.sql 2021-12-27 12:23 1.8K grp.txt.gz 2014-03-02 04:14 208 grp.sql 2014-03-02 04:14 1.4K gold.txt.gz 2010-03-24 14:13 1.7M gold.sql 2010-03-24 14:13 1.7K genscan.txt.gz 2013-12-10 01:52 3.3M genscan.sql 2013-12-10 01:52 1.7K geneid.txt.gz 2015-11-22 18:55 2.6M geneid.sql 2015-11-22 18:55 1.9K gc5Base.txt.gz 2010-03-24 14:22 13M gc5Base.sql 2010-03-24 14:22 1.9K gbLoaded.txt.gz 2020-08-19 14:06 15K gbLoaded.sql 2020-08-19 14:06 1.6K gap.txt.gz 2010-03-24 14:03 1.3M gap.sql 2010-03-24 14:03 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:35 153K ensemblToGeneName.sql 2021-05-25 14:35 1.4K ensemblSource.txt.gz 2021-05-25 14:37 86K ensemblSource.sql 2021-05-25 14:37 1.4K ensPep.txt.gz 2021-05-25 14:37 7.9M ensPep.sql 2021-05-25 14:37 1.3K ensGtp.txt.gz 2021-05-25 14:35 302K ensGtp.sql 2021-05-25 14:35 1.4K ensGene.txt.gz 2021-05-25 14:35 2.3M ensGene.sql 2021-05-25 14:35 1.9K cytoBandIdeo.txt.gz 2013-04-28 18:08 13K cytoBandIdeo.sql 2013-04-28 18:08 1.5K chromInfo.txt.gz 2010-03-24 14:22 13K chromInfo.sql 2010-03-24 14:22 1.3K chromAlias.txt.gz 2018-08-05 08:02 23K chromAlias.sql 2018-08-05 08:02 1.4K chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M chainNeoSch1Link.sql 2020-07-15 21:41 1.5K chainNeoSch1.txt.gz 2020-07-15 21:35 198M chainNeoSch1.sql 2020-07-15 21:35 1.7K chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G chainMonDom5Link.sql 2011-11-21 18:11 1.5K chainMonDom5.txt.gz 2011-11-21 18:25 398M chainMonDom5.sql 2011-11-21 18:23 1.6K chainMm39Link.txt.gz 2020-11-25 04:21 656M chainMm39Link.sql 2020-11-25 04:21 1.6K chainMm39.txt.gz 2020-11-25 04:15 90M chainMm39.sql 2020-11-25 04:15 1.7K chainMm10Link.txt.gz 2017-04-17 01:54 568M chainMm10Link.sql 2017-04-17 01:46 1.5K chainMm10.txt.gz 2013-10-27 17:02 112M chainMm10.sql 2013-10-27 17:02 1.7K chainHg19Link.txt.gz 2010-03-24 14:06 959M chainHg19Link.sql 2010-03-24 14:04 1.5K chainHg19.txt.gz 2010-03-24 14:02 220M chainHg19.sql 2010-03-24 14:01 1.8K blastHg18KG.txt.gz 2010-03-24 14:21 3.9M blastHg18KG.sql 2010-03-24 14:21 2.3K bigFiles.txt.gz 2022-08-07 03:03 73 bigFiles.sql 2022-08-07 03:03 1.4K augustusGene.txt.gz 2015-07-26 16:05 2.3M augustusGene.sql 2015-07-26 16:05 1.9K all_mrna.txt.gz 2019-07-14 07:57 2.1K all_mrna.sql 2019-07-14 07:57 2.1K