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