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