This directory contains a dump of the UCSC genome annotation database for
the May 2010 (Broad AnoCar2.0/anoCar2) assembly of the lizard genome
(anoCar2, Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the lizard genome, see the project website:
http://www.broad.mit.edu/models/anole/

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=anoCar2
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/anoCar2/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/anoCar2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/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 anoCar2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql anoCar2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Lizard sequence is made freely available before scientific publication 
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 particular 
      genes and regions if the provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves the right to publish the initial 
      large-scale analyses of the data set, including large-scale identification 
      of regions of evolutionary conservation and large-scale genomic assembly. 
      Large-scale refers to regions with size on the order of a chromosome (that 
      is, 30 Mb or more).
   4. Any redistribution of the data should carry this notice. 1. The data may 
      be freely downloaded, used in analyses, and repackaged in databases.

All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - netHg19.sql 2011-06-08 10:40 2.0K netHg19.txt.gz 2011-06-08 10:40 9.1M ucscToEnsembl.sql 2011-06-08 10:45 1.3K ucscToEnsembl.txt.gz 2011-06-08 10:45 32K history.sql 2011-06-08 10:45 1.5K history.txt.gz 2011-06-08 10:45 525 chromInfo.sql 2011-06-08 10:46 1.3K chromInfo.txt.gz 2011-06-08 10:46 35K windowmaskerSdust.sql 2011-06-08 10:46 1.4K windowmaskerSdust.txt.gz 2011-06-08 10:46 76M chainGasAcu1Link.sql 2011-06-08 10:47 1.5K chainGasAcu1Link.txt.gz 2011-06-08 10:48 81M netOrnAna1.sql 2011-06-08 10:49 2.0K netOrnAna1.txt.gz 2011-06-08 10:49 8.2M chainGalGal3.sql 2011-06-08 10:52 1.6K chainGalGal3.txt.gz 2011-06-08 10:52 11M blastHg18KG.sql 2011-06-08 10:52 2.1K blastHg18KG.txt.gz 2011-06-08 10:52 2.9M nestedRepeats.sql 2011-06-08 10:52 1.9K nestedRepeats.txt.gz 2011-06-08 10:52 1.4M gold.sql 2011-06-08 10:53 1.6K gold.txt.gz 2011-06-08 10:53 710K chainGasAcu1.sql 2011-06-08 10:53 1.6K chainGasAcu1.txt.gz 2011-06-08 10:53 13M netGalGal3.sql 2011-06-08 11:00 2.0K netGalGal3.txt.gz 2011-06-08 11:00 11M chainOrnAna1.sql 2011-06-08 11:01 1.6K chainOrnAna1.txt.gz 2011-06-08 11:01 12M chainHg19Link.sql 2011-06-08 11:01 1.5K chainHg19Link.txt.gz 2011-06-08 11:02 217M netGasAcu1.sql 2011-06-08 11:04 2.0K netGasAcu1.txt.gz 2011-06-08 11:04 6.1M chainOrnAna1Link.sql 2011-06-08 11:05 1.5K chainOrnAna1Link.txt.gz 2011-06-08 11:05 53M rmsk.sql 2011-06-08 11:05 1.8K rmsk.txt.gz 2011-06-08 11:05 31M chainGalGal3Link.sql 2011-06-08 11:05 1.5K chainGalGal3Link.txt.gz 2011-06-08 11:06 63M chainHg19.sql 2011-06-08 11:06 1.6K chainHg19.txt.gz 2011-06-08 11:06 59M gap.sql 2011-06-08 11:07 1.5K gap.txt.gz 2011-06-08 11:07 492K gc5BaseBw.sql 2011-06-08 11:07 1.2K gc5BaseBw.txt.gz 2011-06-08 11:07 63 simpleRepeat.sql 2011-06-08 11:07 1.9K simpleRepeat.txt.gz 2011-06-08 11:07 19M multiz7way.sql 2011-07-03 07:40 1.5K multiz7way.txt.gz 2011-07-03 07:40 33M multiz7wayFrames.sql 2011-07-03 07:40 1.7K multiz7wayFrames.txt.gz 2011-07-03 07:41 14M extFile.sql 2011-07-03 07:41 1.4K extFile.txt.gz 2011-07-03 07:41 79 multiz7waySummary.sql 2011-07-03 07:41 1.5K multiz7waySummary.txt.gz 2011-07-03 07:41 7.8M cpgIslandExt.sql 2011-10-03 06:42 1.6K cpgIslandExt.txt.gz 2011-10-03 06:42 344K tRNAs.sql 2012-04-22 17:49 1.7K tRNAs.txt.gz 2012-04-22 17:49 5.8K qualityBw.sql 2013-03-17 09:36 1.3K qualityBw.txt.gz 2013-03-17 09:36 63 cytoBandIdeo.sql 2013-04-28 09:53 1.5K cytoBandIdeo.txt.gz 2013-04-28 09:53 35K ucscToINSDC.sql 2013-09-15 08:14 1.4K ucscToINSDC.txt.gz 2013-09-15 08:14 51K chainMm10.sql 2013-10-27 09:19 1.7K chainMm10.txt.gz 2013-10-27 09:19 16M chainMm10Link.sql 2013-10-27 09:19 1.5K chainMm10Link.txt.gz 2013-10-27 09:19 158M netMm10.sql 2013-10-27 09:20 2.1K netMm10.txt.gz 2013-10-27 09:20 8.5M genscan.sql 2013-12-09 18:10 1.7K genscan.txt.gz 2013-12-09 18:10 1.7M grp.sql 2014-03-02 03:37 1.3K grp.txt.gz 2014-03-02 03:37 208 cpgIslandExtUnmasked.sql 2014-06-01 08:03 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:03 883K augustusGene.sql 2015-07-26 09:58 1.9K augustusGene.txt.gz 2015-07-26 09:58 1.9M microsat.sql 2015-08-23 09:36 1.5K microsat.txt.gz 2015-08-23 09:36 903K all_est.sql 2016-06-19 05:08 2.1K all_est.txt.gz 2016-06-19 05:08 9.8M intronEst.sql 2016-06-19 05:08 2.1K intronEst.txt.gz 2016-06-19 05:08 3.5M estOrientInfo.sql 2016-06-19 05:08 1.8K estOrientInfo.txt.gz 2016-06-19 05:08 2.2M chainXenTro9.sql 2017-12-14 08:28 1.7K chainXenTro9.txt.gz 2017-12-14 08:29 45M chainXenTro9Link.sql 2017-12-14 08:29 1.5K chainXenTro9Link.txt.gz 2017-12-14 08:29 213M netXenTro9.sql 2017-12-14 08:30 2.1K netXenTro9.txt.gz 2017-12-14 08:30 8.0M ucscToRefSeq.sql 2018-02-18 05:03 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:03 52K chainGalGal6.sql 2019-01-20 07:54 1.7K chainGalGal6.txt.gz 2019-01-20 07:54 20M chainGalGal6Link.sql 2019-01-20 07:54 1.5K chainGalGal6Link.txt.gz 2019-01-20 07:54 117M netGalGal6.sql 2019-01-20 07:55 2.1K netGalGal6.txt.gz 2019-01-20 07:55 14M mrnaOrientInfo.sql 2019-05-26 04:24 1.8K mrnaOrientInfo.txt.gz 2019-05-26 04:24 3.2K all_mrna.sql 2019-05-26 04:27 2.1K all_mrna.txt.gz 2019-05-26 04:27 11K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 ncbiRefSeq.sql 2020-05-10 03:26 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:26 2.5M ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 241K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 12K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.1M ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.3M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.5M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.0M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 585K xenoMrna.sql 2020-08-18 03:02 2.1K xenoMrna.txt.gz 2020-08-18 03:02 226M xenoRefGene.sql 2020-08-18 03:20 2.0K xenoRefGene.txt.gz 2020-08-18 03:20 26M xenoRefFlat.sql 2020-08-18 03:20 1.7K xenoRefFlat.txt.gz 2020-08-18 03:20 24M xenoRefSeqAli.sql 2020-08-18 03:35 2.1K xenoRefSeqAli.txt.gz 2020-08-18 03:35 25M gbLoaded.sql 2020-08-18 03:38 1.6K gbLoaded.txt.gz 2020-08-18 03:38 114K chromAlias.sql 2021-05-26 11:51 1.4K chromAlias.txt.gz 2021-05-26 11:51 103K ensGene.sql 2021-05-26 12:11 1.9K ensGene.txt.gz 2021-05-26 12:11 2.5M ensGtp.sql 2021-05-26 12:11 1.4K ensGtp.txt.gz 2021-05-26 12:11 421K ensemblToGeneName.sql 2021-05-26 12:11 1.4K ensemblToGeneName.txt.gz 2021-05-26 12:11 118K ensPep.sql 2021-05-26 13:22 1.3K ensPep.txt.gz 2021-05-26 13:22 12M ensemblSource.sql 2021-05-26 13:22 1.4K ensemblSource.txt.gz 2021-05-26 13:22 118K trackDb.sql 2023-12-05 13:52 2.1K trackDb.txt.gz 2023-12-05 13:52 46K hgFindSpec.sql 2023-12-05 13:52 1.8K hgFindSpec.txt.gz 2023-12-05 13:52 1.3K tableDescriptions.sql 2024-11-30 02:03 1.5K tableDescriptions.txt.gz 2024-11-30 02:03 7.3K tableList.sql 2024-12-01 03:31 1.6K tableList.txt.gz 2024-12-01 03:31 4.3K bigFiles.sql 2024-12-01 03:31 1.4K bigFiles.txt.gz 2024-12-01 03:31 107