This directory contains a dump of the UCSC genome annotation database for the Jan. 2018 (Clint_PTRv2/panTro6) assembly of the chimp genome (panTro6, University of Washington) from the Chimp Genome Sequencing Consortium. The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: https://www.ncbi.nlm.nih.gov/genome/202 https://www.ncbi.nlm.nih.gov/genome/assembly/1642151 https://www.ncbi.nlm.nih.gov/bioproject/369439 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=panTro6 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/panTro6/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/panTro6/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/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 panTro6 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql panTro6 --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 - nestedRepeats.sql 2018-10-04 12:44 1.9K nestedRepeats.txt.gz 2018-10-04 12:44 18M all_est.sql 2018-10-04 12:44 2.1K all_est.txt.gz 2018-10-04 12:44 869K netHg38.sql 2018-10-04 12:44 2.1K netHg38.txt.gz 2018-10-04 12:44 6.4M all_mrna.sql 2018-10-04 12:44 2.1K all_mrna.txt.gz 2018-10-04 12:44 297K augustusGene.sql 2018-10-04 12:44 1.9K augustusGene.txt.gz 2018-10-04 12:44 2.3M netMm10.sql 2018-10-04 12:44 2.1K netMm10.txt.gz 2018-10-04 12:45 73M chainHg38.sql 2018-10-04 12:45 1.7K chainHg38.txt.gz 2018-10-04 12:45 67M chainHg38Link.sql 2018-10-04 12:45 1.5K intronEst.sql 2018-10-04 12:45 2.1K intronEst.txt.gz 2018-10-04 12:45 689K chainHg38Link.txt.gz 2018-10-04 12:45 214M chainMm10.sql 2018-10-04 12:46 1.7K refFlat.sql 2018-10-04 12:46 1.7K refFlat.txt.gz 2018-10-04 12:46 201K chainMm10.txt.gz 2018-10-04 12:46 63M chainMm10Link.sql 2018-10-04 12:46 1.5K chainMm10Link.txt.gz 2018-10-04 12:47 515M chromAlias.sql 2018-10-04 12:49 1.4K chromAlias.txt.gz 2018-10-04 12:49 42K chromInfo.sql 2018-10-04 12:49 1.4K chromInfo.txt.gz 2018-10-04 12:49 25K cpgIslandExt.sql 2018-10-04 12:49 1.7K cpgIslandExt.txt.gz 2018-10-04 12:49 634K refGene.sql 2018-10-04 12:49 1.9K refGene.txt.gz 2018-10-04 12:49 218K cpgIslandExtUnmasked.sql 2018-10-04 12:49 1.7K cpgIslandExtUnmasked.txt.gz 2018-10-04 12:49 1.0M cytoBandIdeo.sql 2018-10-04 12:49 1.5K cytoBandIdeo.txt.gz 2018-10-04 12:49 25K grp.sql 2018-10-04 12:49 1.3K grp.txt.gz 2018-10-04 12:49 213 estOrientInfo.sql 2018-10-04 12:49 1.8K estOrientInfo.txt.gz 2018-10-04 12:49 225K gap.sql 2018-10-04 12:49 1.6K gap.txt.gz 2018-10-04 12:49 12K refSeqAli.sql 2018-10-04 12:49 2.1K refSeqAli.txt.gz 2018-10-04 12:49 216K rmsk.sql 2018-10-04 12:49 1.9K rmsk.txt.gz 2018-10-04 12:49 140M gc5BaseBw.sql 2018-10-04 12:50 1.3K gc5BaseBw.txt.gz 2018-10-04 12:50 66 genscan.sql 2018-10-04 12:50 1.7K genscan.txt.gz 2018-10-04 12:50 2.9M simpleRepeat.sql 2018-10-04 12:50 1.9K simpleRepeat.txt.gz 2018-10-04 12:50 27M gold.sql 2018-10-04 12:50 1.7K gold.txt.gz 2018-10-04 12:50 68K microsat.sql 2018-10-04 12:50 1.5K microsat.txt.gz 2018-10-04 12:50 316K mrnaOrientInfo.sql 2018-10-04 12:50 1.8K mrnaOrientInfo.txt.gz 2018-10-04 12:50 111K ucscToINSDC.sql 2018-10-04 12:50 1.4K ucscToINSDC.txt.gz 2018-10-04 12:50 36K ucscToRefSeq.sql 2018-10-04 12:50 1.4K ucscToRefSeq.txt.gz 2018-10-04 12:50 37K windowmaskerSdust.sql 2018-10-04 12:50 1.5K windowmaskerSdust.txt.gz 2018-10-04 12:50 147M xenoMrna.sql 2018-10-04 12:51 2.1K xenoMrna.txt.gz 2018-10-04 12:51 231M xenoRefFlat.sql 2018-10-04 12:52 1.7K xenoRefFlat.txt.gz 2018-10-04 12:52 20M xenoRefGene.sql 2018-10-04 12:52 1.9K xenoRefGene.txt.gz 2018-10-04 12:52 22M xenoRefSeqAli.sql 2018-10-04 12:52 2.1K xenoRefSeqAli.txt.gz 2018-10-04 12:52 19M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 578K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 207K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.6M ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 14M extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.4M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 6.8M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.5M ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 4.5M chainNeoSch1.sql 2020-07-10 06:54 1.7K chainNeoSch1.txt.gz 2020-07-10 06:54 229M chainNeoSch1Link.sql 2020-07-10 07:01 1.6K chainNeoSch1Link.txt.gz 2020-07-10 07:01 882M netNeoSch1.sql 2020-07-10 07:05 2.1K netNeoSch1.txt.gz 2020-07-10 07:05 76M chainMm39.sql 2020-11-24 11:13 1.7K chainMm39.txt.gz 2020-11-24 11:13 64M chainMm39Link.sql 2020-11-24 11:17 1.6K chainMm39Link.txt.gz 2020-11-24 11:17 512M netMm39.sql 2020-11-24 11:20 2.1K netMm39.txt.gz 2020-11-24 11:20 73M trackDb.sql 2024-01-31 15:13 2.1K trackDb.txt.gz 2024-01-31 15:13 51K hgFindSpec.sql 2024-01-31 15:13 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 1.1K tableDescriptions.sql 2024-11-02 02:03 1.5K tableDescriptions.txt.gz 2024-11-02 02:03 6.1K tableList.sql 2024-11-03 03:05 1.6K tableList.txt.gz 2024-11-03 03:05 3.4K bigFiles.sql 2024-11-03 03:05 1.4K bigFiles.txt.gz 2024-11-03 03:05 95