This directory contains a dump of the UCSC genome annotation database for the Nov. 2014 (Charlie1.0/nasLar1) assembly of the proboscis monkey genome (nasLar1, Proboscis Monkey Functional Genome 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/7994 http://www.ncbi.nlm.nih.gov/genome/assembly/221311 http://www.ncbi.nlm.nih.gov/bioproject/241312 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=nasLar1 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/nasLar1/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/nasLar1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/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 nasLar1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql nasLar1 --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 - augustusGene.sql 2017-03-08 13:27 1.9K augustusGene.txt.gz 2017-03-08 13:27 1.7M bigFiles.sql 2024-09-01 03:15 1.4K bigFiles.txt.gz 2024-09-01 03:15 69 chainHg38.sql 2017-03-08 13:27 1.7K chainHg38.txt.gz 2017-03-08 13:29 197M chainHg38Link.sql 2017-03-08 13:36 1.5K chainHg38Link.txt.gz 2017-03-08 13:43 614M chainTarSyr2.sql 2017-03-08 14:03 1.7K chainTarSyr2.txt.gz 2017-03-08 14:06 232M chainTarSyr2Link.sql 2017-03-08 14:14 1.5K chainTarSyr2Link.txt.gz 2017-03-08 14:25 938M chromInfo.sql 2017-03-08 14:54 1.4K chromInfo.txt.gz 2017-03-08 14:54 1.5M cpgIslandExt.sql 2017-03-08 14:54 1.7K cpgIslandExt.txt.gz 2017-03-08 14:54 490K cpgIslandExtUnmasked.sql 2017-03-08 14:54 1.7K cpgIslandExtUnmasked.txt.gz 2017-03-08 14:54 608K cytoBandIdeo.sql 2017-03-08 14:54 1.5K cytoBandIdeo.txt.gz 2017-03-08 14:54 1.5M gap.sql 2017-03-08 14:54 1.6K gap.txt.gz 2017-03-08 14:54 2.9M gbLoaded.sql 2020-08-19 20:19 1.6K gbLoaded.txt.gz 2020-08-19 20:19 5.7K gbStatus.sql 2017-12-31 08:48 1.9K gbStatus.txt.gz 2017-12-31 08:48 3.4M gc5BaseBw.sql 2017-03-08 14:54 1.3K gc5BaseBw.txt.gz 2017-03-08 14:54 66 genscan.sql 2017-03-08 14:54 1.7K genscan.txt.gz 2017-03-08 14:54 2.8M genscanSubopt.sql 2017-03-08 14:59 1.6K genscanSubopt.txt.gz 2017-03-08 14:59 5.2M gold.sql 2017-03-08 15:00 1.7K gold.txt.gz 2017-03-08 15:00 7.7M grp.sql 2017-03-08 15:00 1.3K grp.txt.gz 2017-03-08 15:00 213 hgFindSpec.sql 2024-01-31 15:13 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 569 history.sql 2017-03-08 14:54 1.6K history.txt.gz 2017-03-08 14:54 520 microsat.sql 2017-03-08 13:27 1.5K microsat.txt.gz 2017-03-08 13:27 255K nestedRepeats.sql 2017-03-08 13:36 1.9K nestedRepeats.txt.gz 2017-03-08 13:36 13M netHg38.sql 2017-03-08 15:00 2.1K netHg38.txt.gz 2017-03-08 15:01 28M netTarSyr2.sql 2017-03-08 15:02 2.1K netTarSyr2.txt.gz 2017-03-08 15:04 65M rmsk.sql 2017-03-08 15:05 1.9K rmsk.txt.gz 2017-03-08 15:06 117M simpleRepeat.sql 2017-03-08 14:13 1.9K simpleRepeat.txt.gz 2017-03-08 14:13 18M tableDescriptions.sql 2024-08-31 02:03 1.4K tableDescriptions.txt.gz 2024-08-31 02:03 5.1K tableList.sql 2024-09-01 03:15 1.6K tableList.txt.gz 2024-09-01 03:15 2.1K trackDb.sql 2024-01-31 15:13 2.1K trackDb.txt.gz 2024-01-31 15:13 34K ucscToINSDC.sql 2017-03-08 14:54 1.4K ucscToINSDC.txt.gz 2017-03-08 14:54 2.4M windowmaskerSdust.sql 2017-03-08 14:55 1.5K windowmaskerSdust.txt.gz 2017-03-08 14:56 132M xenoRefFlat.sql 2020-08-19 20:16 1.7K xenoRefFlat.txt.gz 2020-08-19 20:16 27M xenoRefGene.sql 2020-08-19 20:16 2.0K xenoRefGene.txt.gz 2020-08-19 20:16 30M xenoRefSeqAli.sql 2020-08-19 20:16 2.1K xenoRefSeqAli.txt.gz 2020-08-19 20:16 31M