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 - bigFiles.txt.gz 2024-05-19 03:06 73 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 grp.txt.gz 2014-03-02 04:14 208 history.txt.gz 2010-03-24 14:22 573 mrnaOrientInfo.txt.gz 2019-07-14 07:57 958 ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K chromInfo.sql 2010-03-24 14:22 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ensPep.sql 2021-05-25 14:37 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ensemblSource.sql 2021-05-25 14:37 1.4K grp.sql 2014-03-02 04:14 1.4K bigFiles.sql 2024-05-19 03:06 1.4K ensemblToGeneName.sql 2021-05-25 14:35 1.4K hgFindSpec.txt.gz 2023-12-05 13:52 1.4K chromAlias.sql 2018-08-05 08:02 1.4K ucscToINSDC.sql 2013-09-15 15:48 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ensGtp.sql 2021-05-25 14:35 1.4K tableDescriptions.sql 2024-05-18 02:03 1.5K chainMonDom5Link.sql 2011-11-21 18:11 1.5K microsat.sql 2015-08-23 20:42 1.5K cytoBandIdeo.sql 2013-04-28 18:08 1.5K chainHg19Link.sql 2010-03-24 14:04 1.5K chainMm10Link.sql 2017-04-17 01:46 1.5K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K history.sql 2010-03-24 14:22 1.6K chainMm39Link.sql 2020-11-25 04:21 1.6K chainNeoSch1Link.sql 2020-07-15 21:41 1.6K tableList.sql 2024-05-19 03:06 1.6K gbLoaded.sql 2020-08-19 14:06 1.6K gap.sql 2010-03-24 14:03 1.6K chainMonDom5.sql 2011-11-21 18:23 1.6K genscan.sql 2013-12-10 01:52 1.7K tRNAs.sql 2012-04-23 04:53 1.7K chainMm10.sql 2013-10-27 17:02 1.7K gold.sql 2010-03-24 14:13 1.7K chainMm39.sql 2020-11-25 04:15 1.7K refFlat.sql 2020-08-19 14:02 1.7K chainNeoSch1.sql 2020-07-15 21:35 1.7K xenoRefFlat.sql 2020-08-19 14:06 1.7K hgFindSpec.sql 2023-12-05 13:52 1.8K chainHg19.sql 2010-03-24 14:01 1.8K mrnaOrientInfo.sql 2019-07-14 07:57 1.8K gc5Base.sql 2010-03-24 14:22 1.9K quality.sql 2010-03-24 14:12 1.9K geneid.sql 2015-11-22 18:55 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K augustusGene.sql 2015-07-26 16:05 1.9K ensGene.sql 2021-05-25 14:35 1.9K refGene.sql 2020-08-19 14:02 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K xenoRefGene.sql 2020-08-19 14:06 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K rmsk.sql 2010-03-24 14:20 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K nestedRepeats.sql 2010-03-24 14:22 2.0K netMonDom5.sql 2011-11-21 18:27 2.0K simpleRepeat.sql 2010-03-24 14:12 2.0K all_mrna.txt.gz 2019-07-14 07:57 2.1K refFlat.txt.gz 2020-08-19 14:02 2.1K trackDb.sql 2023-12-05 13:52 2.1K netMm10.sql 2013-10-27 17:05 2.1K all_mrna.sql 2019-07-14 07:57 2.1K refSeqAli.sql 2016-09-18 10:07 2.1K netMm39.sql 2020-11-25 04:23 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K netNeoSch1.sql 2020-07-15 21:44 2.1K xenoMrna.sql 2020-08-19 13:31 2.1K xenoRefSeqAli.sql 2020-08-19 14:06 2.1K refGene.txt.gz 2020-08-19 14:02 2.2K blastHg18KG.sql 2010-03-24 14:21 2.3K refSeqAli.txt.gz 2016-09-18 10:07 2.3K netHg19.sql 2010-03-24 14:22 2.3K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K tableList.txt.gz 2024-05-19 03:06 3.8K tableDescriptions.txt.gz 2024-05-18 02:03 6.9K cytoBandIdeo.txt.gz 2013-04-28 18:08 13K chromInfo.txt.gz 2010-03-24 14:22 13K gbLoaded.txt.gz 2020-08-19 14:06 15K ucscToINSDC.txt.gz 2013-09-15 15:48 19K chromAlias.txt.gz 2018-08-05 08:02 23K trackDb.txt.gz 2023-12-05 13:52 30K tRNAs.txt.gz 2012-04-23 04:53 56K ensemblSource.txt.gz 2021-05-25 14:37 86K microsat.txt.gz 2015-08-23 20:42 138K ensemblToGeneName.txt.gz 2021-05-25 14:35 153K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K ensGtp.txt.gz 2021-05-25 14:35 302K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K gap.txt.gz 2010-03-24 14:03 1.3M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M gold.txt.gz 2010-03-24 14:13 1.7M ensGene.txt.gz 2021-05-25 14:35 2.3M augustusGene.txt.gz 2015-07-26 16:05 2.3M geneid.txt.gz 2015-11-22 18:55 2.6M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M genscan.txt.gz 2013-12-10 01:52 3.3M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M blastHg18KG.txt.gz 2010-03-24 14:21 3.9M ensPep.txt.gz 2021-05-25 14:37 7.9M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M simpleRepeat.txt.gz 2010-03-24 14:12 11M gc5Base.txt.gz 2010-03-24 14:22 13M nestedRepeats.txt.gz 2010-03-24 14:22 17M netMonDom5.txt.gz 2011-11-21 18:27 19M xenoRefFlat.txt.gz 2020-08-19 14:06 33M xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M xenoRefGene.txt.gz 2020-08-19 14:06 36M quality.txt.gz 2010-03-24 14:13 55M netMm39.txt.gz 2020-11-25 04:23 58M netMm10.txt.gz 2013-10-27 17:05 58M netHg19.txt.gz 2010-03-24 14:22 74M netNeoSch1.txt.gz 2020-07-15 21:44 77M chainMm39.txt.gz 2020-11-25 04:15 90M chainMm10.txt.gz 2013-10-27 17:02 112M rmsk.txt.gz 2010-03-24 14:20 148M chainNeoSch1.txt.gz 2020-07-15 21:35 198M chainHg19.txt.gz 2010-03-24 14:02 220M xenoMrna.txt.gz 2020-08-19 13:31 302M chainMonDom5.txt.gz 2011-11-21 18:25 398M chainMm10Link.txt.gz 2017-04-17 01:54 568M chainMm39Link.txt.gz 2020-11-25 04:21 656M chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M chainHg19Link.txt.gz 2010-03-24 14:06 959M chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G