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 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 7.3K
tableList.sql 2024-11-24 03:32 1.6K
tableList.txt.gz 2024-11-24 03:32 4.3K
bigFiles.sql 2024-11-24 03:32 1.4K
bigFiles.txt.gz 2024-11-24 03:32 107