This directory contains a dump of the UCSC genome annotation database for the May 2016 (Pan_tro 3.0/panTro5) assembly of the chimp genome (panTro5, Chimpanzee Sequencing and Analysis Consortium) 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: http://www.ncbi.nlm.nih.gov/genome/202 http://www.ncbi.nlm.nih.gov/genome/assembly/733711 http://www.ncbi.nlm.nih.gov/bioproject/10627 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=panTro5 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/panTro5/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/panTro5/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/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 panTro5 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql panTro5 --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 - bigFiles.txt.gz 2024-12-08 03:06 95 bigFiles.sql 2024-12-08 03:06 1.4K tableList.txt.gz 2024-12-08 03:06 3.7K tableList.sql 2024-12-08 03:06 1.6K tableDescriptions.txt.gz 2024-12-07 02:03 6.5K tableDescriptions.sql 2024-12-07 02:03 1.5K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K hgFindSpec.sql 2024-07-25 09:34 1.8K trackDb.txt.gz 2024-07-25 09:34 62K trackDb.sql 2024-07-25 09:34 2.1K ensPep.txt.gz 2021-05-25 14:44 15M ensPep.sql 2021-05-25 14:44 1.3K ensemblSource.txt.gz 2021-05-25 14:44 181K ensemblSource.sql 2021-05-25 14:44 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:43 310K ensemblToGeneName.sql 2021-05-25 14:43 1.4K ensGtp.txt.gz 2021-05-25 14:43 617K ensGtp.sql 2021-05-25 14:43 1.4K ensGene.txt.gz 2021-05-25 14:43 3.5M ensGene.sql 2021-05-25 14:43 1.9K seqNcbiRefSeq.txt.gz 2021-02-10 16:00 1.5M seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K extNcbiRefSeq.txt.gz 2021-02-10 16:00 91 extNcbiRefSeq.sql 2021-02-10 16:00 1.5K ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 13M ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K ncbiRefSeqCds.txt.gz 2021-02-10 16:00 565K ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75 ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K ncbiRefSeqPsl.txt.gz 2021-02-10 15:25 6.6M ncbiRefSeqPsl.sql 2021-02-10 15:25 2.1K ncbiRefSeqLink.txt.gz 2021-02-10 15:25 2.5M ncbiRefSeqLink.sql 2021-02-10 15:25 2.0K ncbiRefSeqPredicted.txt.gz 2021-02-10 15:25 4.4M ncbiRefSeqPredicted.sql 2021-02-10 15:25 2.0K ncbiRefSeqCurated.txt.gz 2021-02-10 15:25 202K ncbiRefSeqCurated.sql 2021-02-10 15:25 2.0K ncbiRefSeq.txt.gz 2021-02-10 15:25 4.5M ncbiRefSeq.sql 2021-02-10 15:25 2.0K gbLoaded.txt.gz 2020-08-22 18:06 38K gbLoaded.sql 2020-08-22 18:06 1.6K xenoRefSeqAli.txt.gz 2020-08-22 18:06 25M xenoRefSeqAli.sql 2020-08-22 18:06 2.1K refSeqAli.txt.gz 2020-08-22 17:50 229K refSeqAli.sql 2020-08-22 17:50 2.1K mrnaOrientInfo.txt.gz 2020-08-22 17:50 115K mrnaOrientInfo.sql 2020-08-22 17:50 1.8K xenoRefFlat.txt.gz 2020-08-22 17:50 24M xenoRefFlat.sql 2020-08-22 17:50 1.7K xenoRefGene.txt.gz 2020-08-22 17:50 27M xenoRefGene.sql 2020-08-22 17:50 2.0K refFlat.txt.gz 2020-08-22 17:50 206K refFlat.sql 2020-08-22 17:50 1.7K refGene.txt.gz 2020-08-22 17:50 225K refGene.sql 2020-08-22 17:50 1.9K xenoMrna.txt.gz 2020-08-22 17:50 257M xenoMrna.sql 2020-08-22 17:50 2.1K all_mrna.txt.gz 2020-08-22 17:50 309K all_mrna.sql 2020-08-22 17:50 2.1K chromAlias.txt.gz 2018-02-04 08:54 467K chromAlias.sql 2018-02-04 08:54 1.4K netRn6.txt.gz 2017-03-28 00:57 82M netRn6.sql 2017-03-28 00:55 2.1K chainRn6Link.txt.gz 2017-03-27 23:19 3.0G chainRn6Link.sql 2017-03-27 22:47 1.5K chainRn6.txt.gz 2017-03-27 22:13 1.0G chainRn6.sql 2017-03-27 22:02 1.7K grp.txt.gz 2016-10-14 15:46 213 grp.sql 2016-10-14 15:46 1.3K windowmaskerSdust.txt.gz 2016-10-14 15:46 161M windowmaskerSdust.sql 2016-10-14 15:46 1.5K ucscToRefSeq.txt.gz 2016-10-14 15:46 353K ucscToRefSeq.sql 2016-10-14 15:46 1.4K gold.txt.gz 2016-10-14 15:46 1.1M gold.sql 2016-10-14 15:46 1.7K gc5BaseBw.txt.gz 2016-10-14 15:46 66 gc5BaseBw.sql 2016-10-14 15:46 1.3K gbMiscDiff.txt.gz 2016-10-14 15:45 1.2M gbMiscDiff.sql 2016-10-14 15:45 1.5K netMm10.txt.gz 2016-10-14 15:45 75M ucscToINSDC.txt.gz 2016-10-14 15:45 362K ucscToINSDC.sql 2016-10-14 15:45 1.4K netMm10.sql 2016-10-14 15:45 2.1K gap.txt.gz 2016-10-14 15:45 364K gap.sql 2016-10-14 15:45 1.6K estOrientInfo.txt.gz 2016-10-14 15:45 231K estOrientInfo.sql 2016-10-14 15:45 1.8K netHg38.txt.gz 2016-10-14 15:45 8.1M netHg38.sql 2016-10-14 15:45 2.1K cytoBandIdeo.txt.gz 2016-10-14 15:45 235K cytoBandIdeo.sql 2016-10-14 15:45 1.5K netGorGor5.txt.gz 2016-10-14 15:45 9.5M netGorGor5.sql 2016-10-14 15:45 2.1K genscan.txt.gz 2016-10-14 15:45 3.1M genscan.sql 2016-10-14 15:45 1.7K cpgIslandExtUnmasked.txt.gz 2016-10-14 15:45 1.1M cpgIslandExtUnmasked.sql 2016-10-14 15:45 1.7K cpgIslandExt.txt.gz 2016-10-14 15:45 707K cpgIslandExt.sql 2016-10-14 15:45 1.7K nestedRepeats.txt.gz 2016-10-14 15:45 19M nestedRepeats.sql 2016-10-14 15:45 1.9K chromInfo.txt.gz 2016-10-14 15:45 218K chromInfo.sql 2016-10-14 15:45 1.4K chainMm10Link.txt.gz 2016-10-14 15:42 542M chainMm10Link.sql 2016-10-14 15:41 1.5K chainMm10.txt.gz 2016-10-14 15:41 67M chainMm10.sql 2016-10-14 15:41 1.7K simpleRepeat.txt.gz 2016-10-14 15:41 31M simpleRepeat.sql 2016-10-14 15:41 1.9K chainHg38Link.txt.gz 2016-10-14 15:40 222M microsat.txt.gz 2016-10-14 15:40 347K microsat.sql 2016-10-14 15:40 1.5K chainHg38Link.sql 2016-10-14 15:40 1.5K chainHg38.txt.gz 2016-10-14 15:39 61M chainHg38.sql 2016-10-14 15:39 1.7K rmsk.txt.gz 2016-10-14 15:39 151M rmsk.sql 2016-10-14 15:38 1.9K chainGorGor5Link.txt.gz 2016-10-14 15:37 253M intronEst.txt.gz 2016-10-14 15:37 705K chainGorGor5Link.sql 2016-10-14 15:37 1.5K intronEst.sql 2016-10-14 15:37 2.1K chainGorGor5.txt.gz 2016-10-14 15:37 83M history.txt.gz 2016-10-14 15:36 614 history.sql 2016-10-14 15:36 1.6K chainGorGor5.sql 2016-10-14 15:36 1.7K augustusGene.txt.gz 2016-10-14 15:36 2.4M augustusGene.sql 2016-10-14 15:36 1.9K all_est.txt.gz 2016-10-14 15:36 889K all_est.sql 2016-10-14 15:36 2.1K