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 - chainRn6Link.txt.gz 2017-03-27 23:19 3.0G chainRn6.txt.gz 2017-03-27 22:13 1.0G chainMm10Link.txt.gz 2016-10-14 15:42 542M xenoMrna.txt.gz 2020-08-22 17:50 257M chainGorGor5Link.txt.gz 2016-10-14 15:37 253M chainHg38Link.txt.gz 2016-10-14 15:40 222M windowmaskerSdust.txt.gz 2016-10-14 15:46 161M rmsk.txt.gz 2016-10-14 15:39 151M chainGorGor5.txt.gz 2016-10-14 15:37 83M netRn6.txt.gz 2017-03-28 00:57 82M netMm10.txt.gz 2016-10-14 15:45 75M chainMm10.txt.gz 2016-10-14 15:41 67M chainHg38.txt.gz 2016-10-14 15:39 61M simpleRepeat.txt.gz 2016-10-14 15:41 31M xenoRefGene.txt.gz 2020-08-22 17:50 27M xenoRefSeqAli.txt.gz 2020-08-22 18:06 25M xenoRefFlat.txt.gz 2020-08-22 17:50 24M nestedRepeats.txt.gz 2016-10-14 15:45 19M ensPep.txt.gz 2021-05-25 14:44 15M ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 13M netGorGor5.txt.gz 2016-10-14 15:45 9.5M netHg38.txt.gz 2016-10-14 15:45 8.1M ncbiRefSeqPsl.txt.gz 2021-02-10 15:25 6.6M ncbiRefSeq.txt.gz 2021-02-10 15:25 4.5M ncbiRefSeqPredicted.txt.gz 2021-02-10 15:25 4.4M ensGene.txt.gz 2021-05-25 14:43 3.5M genscan.txt.gz 2016-10-14 15:45 3.1M ncbiRefSeqLink.txt.gz 2021-02-10 15:25 2.5M augustusGene.txt.gz 2016-10-14 15:36 2.4M seqNcbiRefSeq.txt.gz 2021-02-10 16:00 1.5M gbMiscDiff.txt.gz 2016-10-14 15:45 1.2M cpgIslandExtUnmasked.txt.gz 2016-10-14 15:45 1.1M gold.txt.gz 2016-10-14 15:46 1.1M all_est.txt.gz 2016-10-14 15:36 889K cpgIslandExt.txt.gz 2016-10-14 15:45 707K intronEst.txt.gz 2016-10-14 15:37 705K ensGtp.txt.gz 2021-05-25 14:43 617K ncbiRefSeqCds.txt.gz 2021-02-10 16:00 565K chromAlias.txt.gz 2018-02-04 08:54 467K gap.txt.gz 2016-10-14 15:45 364K ucscToINSDC.txt.gz 2016-10-14 15:45 362K ucscToRefSeq.txt.gz 2016-10-14 15:46 353K microsat.txt.gz 2016-10-14 15:40 347K ensemblToGeneName.txt.gz 2021-05-25 14:43 310K all_mrna.txt.gz 2020-08-22 17:50 309K cytoBandIdeo.txt.gz 2016-10-14 15:45 235K estOrientInfo.txt.gz 2016-10-14 15:45 231K refSeqAli.txt.gz 2020-08-22 17:50 229K refGene.txt.gz 2020-08-22 17:50 225K chromInfo.txt.gz 2016-10-14 15:45 218K refFlat.txt.gz 2020-08-22 17:50 206K ncbiRefSeqCurated.txt.gz 2021-02-10 15:25 202K ensemblSource.txt.gz 2021-05-25 14:44 181K mrnaOrientInfo.txt.gz 2020-08-22 17:50 115K trackDb.txt.gz 2024-07-25 09:34 62K gbLoaded.txt.gz 2020-08-22 18:06 38K tableDescriptions.txt.gz 2024-12-07 02:03 6.5K tableList.txt.gz 2024-12-08 03:06 3.7K xenoRefSeqAli.sql 2020-08-22 18:06 2.1K ncbiRefSeqPsl.sql 2021-02-10 15:25 2.1K refSeqAli.sql 2020-08-22 17:50 2.1K xenoMrna.sql 2020-08-22 17:50 2.1K all_mrna.sql 2020-08-22 17:50 2.1K intronEst.sql 2016-10-14 15:37 2.1K all_est.sql 2016-10-14 15:36 2.1K netGorGor5.sql 2016-10-14 15:45 2.1K netMm10.sql 2016-10-14 15:45 2.1K netHg38.sql 2016-10-14 15:45 2.1K netRn6.sql 2017-03-28 00:55 2.1K trackDb.sql 2024-07-25 09:34 2.1K ncbiRefSeqLink.sql 2021-02-10 15:25 2.0K ncbiRefSeqPredicted.sql 2021-02-10 15:25 2.0K ncbiRefSeqCurated.sql 2021-02-10 15:25 2.0K xenoRefGene.sql 2020-08-22 17:50 2.0K ncbiRefSeq.sql 2021-02-10 15:25 2.0K refGene.sql 2020-08-22 17:50 1.9K ensGene.sql 2021-05-25 14:43 1.9K augustusGene.sql 2016-10-14 15:36 1.9K nestedRepeats.sql 2016-10-14 15:45 1.9K simpleRepeat.sql 2016-10-14 15:41 1.9K rmsk.sql 2016-10-14 15:38 1.9K mrnaOrientInfo.sql 2020-08-22 17:50 1.8K hgFindSpec.sql 2024-07-25 09:34 1.8K estOrientInfo.sql 2016-10-14 15:45 1.8K xenoRefFlat.sql 2020-08-22 17:50 1.7K refFlat.sql 2020-08-22 17:50 1.7K cpgIslandExtUnmasked.sql 2016-10-14 15:45 1.7K chainGorGor5.sql 2016-10-14 15:36 1.7K chainMm10.sql 2016-10-14 15:41 1.7K chainHg38.sql 2016-10-14 15:39 1.7K chainRn6.sql 2017-03-27 22:02 1.7K cpgIslandExt.sql 2016-10-14 15:45 1.7K genscan.sql 2016-10-14 15:45 1.7K gold.sql 2016-10-14 15:46 1.7K gbLoaded.sql 2020-08-22 18:06 1.6K gap.sql 2016-10-14 15:45 1.6K tableList.sql 2024-12-08 03:06 1.6K history.sql 2016-10-14 15:36 1.6K seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K chainGorGor5Link.sql 2016-10-14 15:37 1.5K chainMm10Link.sql 2016-10-14 15:41 1.5K chainHg38Link.sql 2016-10-14 15:40 1.5K chainRn6Link.sql 2017-03-27 22:47 1.5K cytoBandIdeo.sql 2016-10-14 15:45 1.5K windowmaskerSdust.sql 2016-10-14 15:46 1.5K microsat.sql 2016-10-14 15:40 1.5K extNcbiRefSeq.sql 2021-02-10 16:00 1.5K gbMiscDiff.sql 2016-10-14 15:45 1.5K tableDescriptions.sql 2024-12-07 02:03 1.5K ensGtp.sql 2021-05-25 14:43 1.4K ucscToRefSeq.sql 2016-10-14 15:46 1.4K ucscToINSDC.sql 2016-10-14 15:45 1.4K chromAlias.sql 2018-02-04 08:54 1.4K ensemblToGeneName.sql 2021-05-25 14:43 1.4K bigFiles.sql 2024-12-08 03:06 1.4K chromInfo.sql 2016-10-14 15:45 1.4K ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K ensemblSource.sql 2021-05-25 14:44 1.4K ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K grp.sql 2016-10-14 15:46 1.3K ensPep.sql 2021-05-25 14:44 1.3K ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K gc5BaseBw.sql 2016-10-14 15:46 1.3K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K history.txt.gz 2016-10-14 15:36 614 grp.txt.gz 2016-10-14 15:46 213 bigFiles.txt.gz 2024-12-08 03:06 95 extNcbiRefSeq.txt.gz 2021-02-10 16:00 91 ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75 gc5BaseBw.txt.gz 2016-10-14 15:46 66