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