This directory contains a dump of the UCSC genome annotation database for the Aug. 2016 (Xenopus_laevis_v2/xenLae2) assembly of the african clawed frog genome (xenLae2, International Xenopus Sequencing Consortium) . The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/81 http://www.ncbi.nlm.nih.gov/genome/assembly/779791 http://www.ncbi.nlm.nih.gov/bioproject/338693 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=xenLae2 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.soe.ucsc.edu, then go to the directory goldenPath/xenLae2/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.soe.ucsc.edu/goldenPath/xenLae2/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/database/gc5Base.txt.gz' -O gc5Base.txt.gz 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 xenLae2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql xenLae2 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. ----------------------------------------------------------------------------- All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - augustusGene.sql 2017-11-15 13:09 1.9K augustusGene.txt.gz 2017-11-15 13:09 3.4M rmsk.sql 2017-11-15 13:09 1.9K rmsk.txt.gz 2017-11-15 13:09 44M chainHg38.sql 2017-11-15 13:09 1.7K chainHg38.txt.gz 2017-11-15 13:09 63M chainHg38Link.sql 2017-11-15 13:10 1.5K history.sql 2017-11-15 13:10 1.6K history.txt.gz 2017-11-15 13:10 655 chainHg38Link.txt.gz 2017-11-15 13:10 291M simpleRepeat.sql 2017-11-15 13:11 1.9K simpleRepeat.txt.gz 2017-11-15 13:11 21M chainMm10.sql 2017-11-15 13:11 1.7K chainMm10.txt.gz 2017-11-15 13:11 33M chainMm10Link.sql 2017-11-15 13:11 1.5K chainMm10Link.txt.gz 2017-11-15 13:12 290M chainXenTro9.sql 2017-11-15 13:13 1.7K microsat.sql 2017-11-15 13:13 1.5K microsat.txt.gz 2017-11-15 13:13 105K chainXenTro9.txt.gz 2017-11-15 13:15 1.6G chainXenTro9Link.sql 2017-11-15 13:20 1.5K chainXenTro9Link.txt.gz 2017-11-15 13:25 3.5G nestedRepeats.sql 2017-11-15 13:38 1.9K nestedRepeats.txt.gz 2017-11-15 13:38 2.9M chromAlias.sql 2017-11-15 13:38 1.4K chromAlias.txt.gz 2017-11-15 13:38 1.0M chromInfo.sql 2017-11-15 13:38 1.4K chromInfo.txt.gz 2017-11-15 13:38 346K netHg38.sql 2017-11-15 13:38 2.1K netHg38.txt.gz 2017-11-15 13:38 12M cpgIslandExt.sql 2017-11-15 13:38 1.7K cpgIslandExt.txt.gz 2017-11-15 13:38 262K cpgIslandExtUnmasked.sql 2017-11-15 13:38 1.7K cpgIslandExtUnmasked.txt.gz 2017-11-15 13:38 1.7M genscan.sql 2017-11-15 13:38 1.7K genscan.txt.gz 2017-11-15 13:38 2.9M netMm10.sql 2017-11-15 13:38 2.1K netMm10.txt.gz 2017-11-15 13:38 12M cytoBandIdeo.sql 2017-11-15 13:38 1.5K cytoBandIdeo.txt.gz 2017-11-15 13:38 271K netXenTro9.sql 2017-11-15 13:38 2.1K netXenTro9.txt.gz 2017-11-15 13:38 111M gap.sql 2017-11-15 13:39 1.6K gap.txt.gz 2017-11-15 13:39 3.0M ucscToINSDC.sql 2017-11-15 13:39 1.4K ucscToINSDC.txt.gz 2017-11-15 13:39 551K gc5BaseBw.sql 2017-11-15 13:39 1.3K gc5BaseBw.txt.gz 2017-11-15 13:39 66 gold.sql 2017-11-15 13:39 1.7K gold.txt.gz 2017-11-15 13:39 4.4M ucscToRefSeq.sql 2017-11-15 13:39 1.4K ucscToRefSeq.txt.gz 2017-11-15 13:39 549K windowmaskerSdust.sql 2017-11-15 13:39 1.5K windowmaskerSdust.txt.gz 2017-11-15 13:39 129M grp.sql 2017-11-15 13:39 1.3K grp.txt.gz 2017-11-15 13:39 213 all_est.sql 2018-10-21 09:23 2.1K all_est.txt.gz 2018-10-21 09:23 38M intronEst.sql 2018-10-21 09:24 2.1K intronEst.txt.gz 2018-10-21 09:24 25M estOrientInfo.sql 2018-10-21 09:24 1.8K estOrientInfo.txt.gz 2018-10-21 09:24 8.8M netGalGal6.sql 2019-01-20 20:25 2.1K netGalGal6.txt.gz 2019-01-20 20:25 13M chainGalGal6.sql 2019-01-20 20:25 1.7K chainGalGal6.txt.gz 2019-01-20 20:25 12M chainGalGal6Link.sql 2019-01-20 20:25 1.5K chainGalGal6Link.txt.gz 2019-01-20 20:25 65M extNcbiRefSeq.sql 2020-05-10 03:29 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:29 91 ncbiRefSeq.sql 2020-05-10 03:29 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:29 4.2M ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:29 386K ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 1.1M ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.9M ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75 ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 12M ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 3.4M ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 5.3M seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:29 921K all_mrna.sql 2020-08-20 18:26 2.1K all_mrna.txt.gz 2020-08-20 18:26 2.0M refGene.sql 2020-08-20 18:30 1.9K refGene.txt.gz 2020-08-20 18:30 1.2M refFlat.sql 2020-08-20 18:42 1.7K refFlat.txt.gz 2020-08-20 18:42 1.1M xenoRefGene.sql 2020-08-20 18:42 2.0K xenoRefGene.txt.gz 2020-08-20 18:42 21M xenoRefFlat.sql 2020-08-20 18:44 1.7K xenoRefFlat.txt.gz 2020-08-20 18:44 18M mrnaOrientInfo.sql 2020-08-20 18:44 1.8K mrnaOrientInfo.txt.gz 2020-08-20 18:44 611K refSeqAli.sql 2020-08-20 18:44 2.1K refSeqAli.txt.gz 2020-08-20 18:44 1.2M xenoRefSeqAli.sql 2020-08-20 18:44 2.1K xenoRefSeqAli.txt.gz 2020-08-20 18:44 18M gbLoaded.sql 2020-08-20 18:44 1.6K gbLoaded.txt.gz 2020-08-20 18:44 32K trackDb.sql 2023-12-05 13:52 2.1K trackDb.txt.gz 2023-12-05 13:52 34K hgFindSpec.sql 2023-12-05 13:52 1.8K hgFindSpec.txt.gz 2023-12-05 13:52 1.1K tableDescriptions.sql 2024-10-12 02:03 1.5K tableDescriptions.txt.gz 2024-10-12 02:03 6.3K tableList.sql 2024-10-13 03:07 1.6K tableList.txt.gz 2024-10-13 03:07 3.4K bigFiles.sql 2024-10-13 03:07 1.4K bigFiles.txt.gz 2024-10-13 03:07 95