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 2024-10-06 03:31 107 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 2024-10-06 03:31 1.4K ensemblToGeneName.sql 2021-05-26 12:11 1.4K tableDescriptions.sql 2024-10-05 02:03 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 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 2024-10-06 03:31 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 2024-10-06 03:31 4.3K tRNAs.txt.gz 2012-04-22 17:49 5.8K tableDescriptions.txt.gz 2024-10-05 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