This directory contains a dump of the UCSC genome annotation database for the Feb. 2019 (Mmul_10/rheMac10) assembly of the rhesus genome (rheMac10, The Genome Institute at Washington University School of Medicine) . 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/215 https://www.ncbi.nlm.nih.gov/genome/assembly/2345051 https://www.ncbi.nlm.nih.gov/bioproject/476474 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=rheMac10 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/rheMac10/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/rheMac10/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/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 rheMac10 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql rheMac10 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' The Rhesus sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of these data are properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. ----------------------------------------------------------------------------- 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 - ncbiRefSeqLink.sql 2019-09-03 15:27 2.0K all_est.sql 2019-09-03 15:27 2.1K all_est.txt.gz 2019-09-03 15:27 4.0M ncbiRefSeqLink.txt.gz 2019-09-03 15:27 2.3M all_mrna.sql 2019-09-03 15:27 2.1K ncbiRefSeqOther.sql 2019-09-03 15:27 1.3K ncbiRefSeqOther.txt.gz 2019-09-03 15:27 76 all_mrna.txt.gz 2019-09-03 15:27 16M augustusGene.sql 2019-09-03 15:27 1.9K augustusGene.txt.gz 2019-09-03 15:27 2.3M ncbiRefSeqPsl.sql 2019-09-03 15:27 2.1K ncbiRefSeqPsl.txt.gz 2019-09-03 15:27 5.9M chainHg19.sql 2019-09-03 15:27 1.7K chainHg19.txt.gz 2019-09-03 15:27 19M chainHg19Link.sql 2019-09-03 15:27 1.5K chainHg19Link.txt.gz 2019-09-03 15:28 205M nestedRepeats.sql 2019-09-03 15:28 1.9K nestedRepeats.txt.gz 2019-09-03 15:28 18M chainHg38.sql 2019-09-03 15:29 1.7K chainHg38.txt.gz 2019-09-03 15:29 21M netHg19.sql 2019-09-03 15:29 2.1K netHg19.txt.gz 2019-09-03 15:29 22M chainHg38Link.sql 2019-09-03 15:29 1.5K history.sql 2019-09-03 15:29 1.6K history.txt.gz 2019-09-03 15:29 941 chainHg38Link.txt.gz 2019-09-03 15:29 210M chainMm10.sql 2019-09-03 15:30 1.7K chainMm10.txt.gz 2019-09-03 15:30 67M chainMm10Link.sql 2019-09-03 15:30 1.5K intronEst.sql 2019-09-03 15:30 2.1K intronEst.txt.gz 2019-09-03 15:30 2.2M chainMm10Link.txt.gz 2019-09-03 15:31 514M chromAlias.sql 2019-09-03 15:33 1.4K chromAlias.txt.gz 2019-09-03 15:33 28K microsat.sql 2019-09-03 15:33 1.5K microsat.txt.gz 2019-09-03 15:33 352K netHg38.sql 2019-09-03 15:33 2.1K netHg38.txt.gz 2019-09-03 15:33 22M chromInfo.sql 2019-09-03 15:33 1.4K chromInfo.txt.gz 2019-09-03 15:33 19K mrnaOrientInfo.sql 2019-09-03 15:33 1.8K mrnaOrientInfo.txt.gz 2019-09-03 15:33 4.2M cpgIslandExt.sql 2019-09-03 15:33 1.7K cpgIslandExt.txt.gz 2019-09-03 15:33 634K cpgIslandExtUnmasked.sql 2019-09-03 15:33 1.7K cpgIslandExtUnmasked.txt.gz 2019-09-03 15:33 1.6M ncbiRefSeq.sql 2019-09-03 15:33 1.9K ncbiRefSeq.txt.gz 2019-09-03 15:33 4.1M cytoBandIdeo.sql 2019-09-03 15:33 1.5K cytoBandIdeo.txt.gz 2019-09-03 15:33 18K estOrientInfo.sql 2019-09-03 15:33 1.8K estOrientInfo.txt.gz 2019-09-03 15:33 937K extNcbiRefSeq.sql 2019-09-03 15:33 1.4K extNcbiRefSeq.txt.gz 2019-09-03 15:33 89 ncbiRefSeqCds.sql 2019-09-03 15:33 1.3K ncbiRefSeqCds.txt.gz 2019-09-03 15:33 469K ncbiRefSeqCurated.sql 2019-09-03 15:33 2.0K ncbiRefSeqCurated.txt.gz 2019-09-03 15:33 550K netMm10.sql 2019-09-03 15:33 2.1K netMm10.txt.gz 2019-09-03 15:33 72M gap.sql 2019-09-03 15:33 1.6K gap.txt.gz 2019-09-03 15:33 4.1K gapOverlap.sql 2019-09-03 15:33 1.8K gapOverlap.txt.gz 2019-09-03 15:33 91 gbLoaded.sql 2019-09-03 15:33 1.6K gbLoaded.txt.gz 2019-09-03 15:33 944 gc5BaseBw.sql 2019-09-03 15:33 1.3K gc5BaseBw.txt.gz 2019-09-03 15:33 67 genscan.sql 2019-09-03 15:33 1.7K genscan.txt.gz 2019-09-03 15:33 2.9M refFlat.sql 2019-09-03 15:33 1.7K refFlat.txt.gz 2019-09-03 15:33 503K gold.sql 2019-09-03 15:33 1.7K gold.txt.gz 2019-09-03 15:33 41K grp.sql 2019-09-03 15:33 1.3K grp.txt.gz 2019-09-03 15:33 213 refGene.sql 2019-09-03 15:33 1.9K refGene.txt.gz 2019-09-03 15:33 552K refSeqAli.sql 2019-09-03 15:33 2.1K refSeqAli.txt.gz 2019-09-03 15:33 563K rmsk.sql 2019-09-03 15:33 1.9K rmsk.txt.gz 2019-09-03 15:33 141M ncbiRefSeqPepTable.sql 2019-09-03 15:34 1.4K ncbiRefSeqPepTable.txt.gz 2019-09-03 15:34 12M ncbiRefSeqPredicted.sql 2019-09-03 15:34 2.0K ncbiRefSeqPredicted.txt.gz 2019-09-03 15:34 3.8M seqNcbiRefSeq.sql 2019-09-03 15:34 1.5K seqNcbiRefSeq.txt.gz 2019-09-03 15:34 1.3M simpleRepeat.sql 2019-09-03 15:34 1.9K simpleRepeat.txt.gz 2019-09-03 15:34 26M tandemDups.sql 2019-09-03 15:34 1.8K tandemDups.txt.gz 2019-09-03 15:34 30M ucscToINSDC.sql 2019-09-03 15:34 1.4K ucscToINSDC.txt.gz 2019-09-03 15:34 25K ucscToRefSeq.sql 2019-09-03 15:34 1.4K ucscToRefSeq.txt.gz 2019-09-03 15:34 25K windowmaskerSdust.sql 2019-09-03 15:34 1.5K windowmaskerSdust.txt.gz 2019-09-03 15:34 146M xenoRefFlat.sql 2019-09-03 15:35 1.7K xenoRefFlat.txt.gz 2019-09-03 15:35 14M xenoRefGene.sql 2019-09-03 15:35 1.9K xenoRefGene.txt.gz 2019-09-03 15:35 16M xenoRefSeqAli.sql 2019-09-03 15:35 2.1K xenoRefSeqAli.txt.gz 2019-09-03 15:35 22M rhesusSNVs.sql 2020-05-19 14:27 1.3K rhesusSNVs.txt.gz 2020-05-19 14:27 72 chainNeoSch1.sql 2020-07-12 01:20 1.7K chainNeoSch1.txt.gz 2020-07-12 01:20 206M chainNeoSch1Link.sql 2020-07-12 01:26 1.6K chainNeoSch1Link.txt.gz 2020-07-12 01:26 846M netNeoSch1.sql 2020-07-12 01:29 2.1K netNeoSch1.txt.gz 2020-07-12 01:29 77M chainMm39.sql 2020-10-21 09:09 1.7K chainMm39.txt.gz 2020-10-21 09:09 64M chainMm39Link.sql 2020-10-21 09:12 1.6K chainMm39Link.txt.gz 2020-10-21 09:12 500M netMm39.sql 2020-10-21 09:16 2.1K netMm39.txt.gz 2020-10-21 09:16 72M ensGene.sql 2021-05-25 14:47 1.9K ensGene.txt.gz 2021-05-25 14:47 3.6M ensGtp.sql 2021-05-25 14:47 1.4K ensGtp.txt.gz 2021-05-25 14:47 673K ensemblToGeneName.sql 2021-05-25 14:47 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:47 322K ensemblSource.sql 2021-05-25 14:49 1.4K ensemblSource.txt.gz 2021-05-25 14:49 197K ensPep.sql 2021-05-25 14:49 1.3K ensPep.txt.gz 2021-05-25 14:49 16M trackDb.sql 2024-07-25 09:34 2.1K trackDb.txt.gz 2024-07-25 09:34 72K hgFindSpec.sql 2024-07-25 09:34 1.8K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K tableDescriptions.sql 2024-11-02 02:04 1.5K tableDescriptions.txt.gz 2024-11-02 02:04 6.7K tableList.sql 2024-11-03 03:05 1.6K tableList.txt.gz 2024-11-03 03:05 3.8K bigFiles.sql 2024-11-03 03:05 1.4K bigFiles.txt.gz 2024-11-03 03:05 124