This directory contains a dump of the UCSC genome annotation database for the Apr. 2017 (Panu_3.0/papAnu4) assembly of the baboon genome (papAnu4, Human Genome Sequencing Center) . 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/394 https://www.ncbi.nlm.nih.gov/genome/assembly/1082401 https://www.ncbi.nlm.nih.gov/bioproject/54005 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=papAnu4 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/papAnu4/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/papAnu4/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/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 papAnu4 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql papAnu4 --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 - gc5BaseBw.txt.gz 2019-06-25 11:38 66 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 bigFiles.txt.gz 2024-09-01 03:06 95 grp.txt.gz 2019-06-25 11:27 213 history.txt.gz 2019-06-25 11:37 817 hgFindSpec.txt.gz 2023-12-05 13:51 1.3K gc5BaseBw.sql 2019-06-25 11:38 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ensPep.sql 2021-05-25 14:43 1.3K grp.sql 2019-06-25 11:27 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ensemblSource.sql 2021-05-25 14:43 1.4K bigFiles.sql 2024-09-01 03:06 1.4K chromInfo.sql 2019-06-25 11:37 1.4K ensemblToGeneName.sql 2021-05-25 14:43 1.4K chromAlias.sql 2019-06-25 11:37 1.4K ucscToINSDC.sql 2019-06-25 11:38 1.4K tableDescriptions.sql 2024-08-31 02:04 1.4K ucscToRefSeq.sql 2019-06-25 11:38 1.4K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ensGtp.sql 2021-05-25 14:43 1.4K microsat.sql 2019-06-25 11:38 1.5K windowmaskerSdust.sql 2019-06-25 11:38 1.5K cytoBandIdeo.sql 2019-06-25 11:38 1.5K chainHg38Link.sql 2019-06-25 11:27 1.5K chainMm10Link.sql 2019-06-25 11:34 1.5K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K tableList.sql 2024-09-01 03:06 1.6K history.sql 2019-06-25 11:37 1.6K gbLoaded.sql 2019-06-25 11:38 1.6K gap.sql 2019-06-25 11:38 1.6K gold.sql 2019-06-25 11:38 1.7K genscan.sql 2019-06-25 11:38 1.7K cpgIslandExt.sql 2019-06-25 11:38 1.7K chainHg38.sql 2019-06-25 11:25 1.7K chainMm10.sql 2019-06-25 11:34 1.7K refFlat.sql 2019-06-25 11:25 1.7K cpgIslandExtUnmasked.sql 2019-06-25 11:38 1.7K xenoRefFlat.sql 2019-06-25 11:39 1.7K hgFindSpec.sql 2023-12-05 13:51 1.8K estOrientInfo.sql 2019-06-25 11:38 1.8K mrnaOrientInfo.sql 2019-06-25 11:38 1.8K rmsk.sql 2019-06-25 11:37 1.9K refGene.sql 2019-06-25 11:27 1.9K simpleRepeat.sql 2019-06-25 11:38 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K nestedRepeats.sql 2019-06-25 11:38 1.9K xenoRefGene.sql 2019-06-25 11:39 1.9K augustusGene.sql 2019-06-25 11:25 1.9K ensGene.sql 2021-05-25 14:43 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K trackDb.sql 2023-12-05 13:51 2.1K netHg38.sql 2019-06-25 11:38 2.1K netMm10.sql 2019-06-25 11:24 2.1K all_est.sql 2019-06-25 11:24 2.1K all_mrna.sql 2019-06-25 11:25 2.1K intronEst.sql 2019-06-25 11:37 2.1K refSeqAli.sql 2019-06-25 11:34 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K xenoRefSeqAli.sql 2019-06-25 11:39 2.1K tableList.txt.gz 2024-09-01 03:06 3.2K tableDescriptions.txt.gz 2024-08-31 02:04 6.3K gbLoaded.txt.gz 2019-06-25 11:38 12K mrnaOrientInfo.txt.gz 2019-06-25 11:38 17K trackDb.txt.gz 2023-12-05 13:51 32K all_mrna.txt.gz 2019-06-25 11:25 34K refFlat.txt.gz 2019-06-25 11:25 41K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 44K refGene.txt.gz 2019-06-25 11:27 45K refSeqAli.txt.gz 2019-06-25 11:34 47K ensemblSource.txt.gz 2021-05-25 14:43 158K ensemblToGeneName.txt.gz 2021-05-25 14:43 264K microsat.txt.gz 2019-06-25 11:38 312K cytoBandIdeo.txt.gz 2019-06-25 11:38 320K chromInfo.txt.gz 2019-06-25 11:37 328K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 473K ucscToRefSeq.txt.gz 2019-06-25 11:38 496K ucscToINSDC.txt.gz 2019-06-25 11:38 506K ensGtp.txt.gz 2021-05-25 14:43 522K chromAlias.txt.gz 2019-06-25 11:37 651K cpgIslandExt.txt.gz 2019-06-25 11:38 660K gap.txt.gz 2019-06-25 11:38 703K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.3M gold.txt.gz 2019-06-25 11:38 1.6M estOrientInfo.txt.gz 2019-06-25 11:38 1.7M cpgIslandExtUnmasked.txt.gz 2019-06-25 11:38 1.8M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.2M augustusGene.txt.gz 2019-06-25 11:25 2.3M genscan.txt.gz 2019-06-25 11:38 2.9M intronEst.txt.gz 2019-06-25 11:37 3.0M ensGene.txt.gz 2021-05-25 14:43 3.1M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.0M ncbiRefSeq.txt.gz 2020-05-10 03:28 4.0M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.7M all_est.txt.gz 2019-06-25 11:24 6.0M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 12M ensPep.txt.gz 2021-05-25 14:43 14M nestedRepeats.txt.gz 2019-06-25 11:38 18M xenoRefFlat.txt.gz 2019-06-25 11:39 22M xenoRefSeqAli.txt.gz 2019-06-25 11:39 23M xenoRefGene.txt.gz 2019-06-25 11:39 25M netHg38.txt.gz 2019-06-25 11:38 28M simpleRepeat.txt.gz 2019-06-25 11:38 30M chainMm10.txt.gz 2019-06-25 11:34 65M netMm10.txt.gz 2019-06-25 11:24 71M rmsk.txt.gz 2019-06-25 11:37 143M windowmaskerSdust.txt.gz 2019-06-25 11:38 147M chainMm10Link.txt.gz 2019-06-25 11:35 501M chainHg38.txt.gz 2019-06-25 11:25 541M chainHg38Link.txt.gz 2019-06-25 11:29 1.5G