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 - all_est.sql 2016-06-19 05:08 2.1K all_est.txt.gz 2016-06-19 05:08 9.8M all_mrna.sql 2019-05-26 04:27 2.1K all_mrna.txt.gz 2019-05-26 04:27 11K augustusGene.sql 2015-07-26 09:58 1.9K augustusGene.txt.gz 2015-07-26 09:58 1.9M bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 107 blastHg18KG.sql 2011-06-08 10:52 2.1K blastHg18KG.txt.gz 2011-06-08 10:52 2.9M chainGalGal3.sql 2011-06-08 10:52 1.6K chainGalGal3.txt.gz 2011-06-08 10:52 11M chainGalGal3Link.sql 2011-06-08 11:05 1.5K chainGalGal3Link.txt.gz 2011-06-08 11:06 63M 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 chainGasAcu1.sql 2011-06-08 10:53 1.6K chainGasAcu1.txt.gz 2011-06-08 10:53 13M chainGasAcu1Link.sql 2011-06-08 10:47 1.5K chainGasAcu1Link.txt.gz 2011-06-08 10:48 81M chainHg19.sql 2011-06-08 11:06 1.6K chainHg19.txt.gz 2011-06-08 11:06 59M chainHg19Link.sql 2011-06-08 11:01 1.5K chainHg19Link.txt.gz 2011-06-08 11:02 217M 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 chainOrnAna1.sql 2011-06-08 11:01 1.6K chainOrnAna1.txt.gz 2011-06-08 11:01 12M chainOrnAna1Link.sql 2011-06-08 11:05 1.5K chainOrnAna1Link.txt.gz 2011-06-08 11:05 53M 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 chromAlias.sql 2018-02-18 05:03 1.4K chromAlias.txt.gz 2018-02-18 05:03 88K chromInfo.sql 2011-06-08 10:46 1.3K chromInfo.txt.gz 2011-06-08 10:46 35K cpgIslandExt.sql 2011-10-03 06:42 1.6K cpgIslandExt.txt.gz 2011-10-03 06:42 344K cpgIslandExtUnmasked.sql 2014-06-01 08:03 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:03 883K cytoBandIdeo.sql 2013-04-28 09:53 1.5K cytoBandIdeo.txt.gz 2013-04-28 09:53 35K ensGene.sql 2020-08-31 15:14 1.9K ensGene.txt.gz 2020-08-31 15:14 2.1M ensGtp.sql 2020-08-31 15:14 1.4K ensGtp.txt.gz 2020-08-31 15:14 284K ensPep.sql 2020-08-31 15:39 1.3K ensPep.txt.gz 2020-08-31 15:39 5.7M ensemblSource.sql 2020-08-31 15:39 1.4K ensemblSource.txt.gz 2020-08-31 15:39 84K ensemblToGeneName.sql 2020-08-31 15:14 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:14 105K estOrientInfo.sql 2016-06-19 05:08 1.8K estOrientInfo.txt.gz 2016-06-19 05:08 2.2M extFile.sql 2011-07-03 07:41 1.4K extFile.txt.gz 2011-07-03 07:41 79 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 gap.sql 2011-06-08 11:07 1.5K gap.txt.gz 2011-06-08 11:07 492K gbLoaded.sql 2020-08-18 03:38 1.6K gbLoaded.txt.gz 2020-08-18 03:38 114K gc5BaseBw.sql 2011-06-08 11:07 1.2K gc5BaseBw.txt.gz 2011-06-08 11:07 63 genscan.sql 2013-12-09 18:10 1.7K genscan.txt.gz 2013-12-09 18:10 1.7M gold.sql 2011-06-08 10:53 1.6K gold.txt.gz 2011-06-08 10:53 710K grp.sql 2014-03-02 03:37 1.3K grp.txt.gz 2014-03-02 03:37 208 hgFindSpec.sql 2020-12-06 07:37 1.7K hgFindSpec.txt.gz 2020-12-06 07:37 1.2K history.sql 2011-06-08 10:45 1.5K history.txt.gz 2011-06-08 10:45 525 intronEst.sql 2016-06-19 05:08 2.1K intronEst.txt.gz 2016-06-19 05:08 3.5M microsat.sql 2015-08-23 09:36 1.5K microsat.txt.gz 2015-08-23 09:36 903K mrnaOrientInfo.sql 2019-05-26 04:24 1.8K mrnaOrientInfo.txt.gz 2019-05-26 04:24 3.2K 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 multiz7waySummary.sql 2011-07-03 07:41 1.5K multiz7waySummary.txt.gz 2011-07-03 07:41 7.8M 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 nestedRepeats.sql 2011-06-08 10:52 1.9K nestedRepeats.txt.gz 2011-06-08 10:52 1.4M netGalGal3.sql 2011-06-08 11:00 2.0K netGalGal3.txt.gz 2011-06-08 11:00 11M netGalGal6.sql 2019-01-20 07:55 2.1K netGalGal6.txt.gz 2019-01-20 07:55 14M netGasAcu1.sql 2011-06-08 11:04 2.0K netGasAcu1.txt.gz 2011-06-08 11:04 6.1M netHg19.sql 2011-06-08 10:40 2.0K netHg19.txt.gz 2011-06-08 10:40 9.1M netMm10.sql 2013-10-27 09:20 2.1K netMm10.txt.gz 2013-10-27 09:20 8.5M netOrnAna1.sql 2011-06-08 10:49 2.0K netOrnAna1.txt.gz 2011-06-08 10:49 8.2M netXenTro9.sql 2017-12-14 08:30 2.1K netXenTro9.txt.gz 2017-12-14 08:30 8.0M qualityBw.sql 2013-03-17 09:36 1.3K qualityBw.txt.gz 2013-03-17 09:36 63 rmsk.sql 2011-06-08 11:05 1.8K rmsk.txt.gz 2011-06-08 11:05 31M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 585K simpleRepeat.sql 2011-06-08 11:07 1.9K simpleRepeat.txt.gz 2011-06-08 11:07 19M tRNAs.sql 2012-04-22 17:49 1.7K tRNAs.txt.gz 2012-04-22 17:49 5.8K tableDescriptions.sql 2020-04-26 03:23 1.4K tableDescriptions.txt.gz 2020-04-26 03:23 7.3K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 4.3K trackDb.sql 2020-12-05 08:30 2.0K trackDb.txt.gz 2020-12-05 08:30 57K ucscToEnsembl.sql 2011-06-08 10:45 1.3K ucscToEnsembl.txt.gz 2011-06-08 10:45 32K ucscToINSDC.sql 2013-09-15 08:14 1.4K ucscToINSDC.txt.gz 2013-09-15 08:14 51K ucscToRefSeq.sql 2018-02-18 05:03 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:03 52K windowmaskerSdust.sql 2011-06-08 10:46 1.4K windowmaskerSdust.txt.gz 2011-06-08 10:46 76M xenoMrna.sql 2020-08-18 03:02 2.1K xenoMrna.txt.gz 2020-08-18 03:02 226M xenoRefFlat.sql 2020-08-18 03:20 1.7K xenoRefFlat.txt.gz 2020-08-18 03:20 24M xenoRefGene.sql 2020-08-18 03:20 1.9K xenoRefGene.txt.gz 2020-08-18 03:20 26M xenoRefSeqAli.sql 2020-08-18 03:35 2.1K xenoRefSeqAli.txt.gz 2020-08-18 03:35 25M