This directory contains a dump of the UCSC genome annotation database for the Jun. 2014 (G_variegatus-3.0.2/galVar1) assembly of the malayan flying lemur genome (galVar1, Washington University (WashU)) . 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/792 http://www.ncbi.nlm.nih.gov/genome/assembly/182621 http://www.ncbi.nlm.nih.gov/bioproject/253111 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=galVar1 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/galVar1/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/galVar1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/galVar1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galVar1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/galVar1/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 galVar1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql galVar1 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' The Malayan flying lemur 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 - augustusGene.sql 2016-08-15 13:07 1.9K augustusGene.txt.gz 2016-08-15 13:07 3.0M author.sql 2016-08-15 13:07 1.4K author.txt.gz 2016-08-15 13:07 2.9M bigFiles.sql 2024-09-01 03:12 1.4K bigFiles.txt.gz 2024-09-01 03:12 95 cds.sql 2016-08-15 13:07 1.4K cds.txt.gz 2016-08-15 13:07 1.7M cell.sql 2016-08-15 13:07 1.4K cell.txt.gz 2016-08-15 13:07 40 chainCavPor3.sql 2016-08-15 13:07 1.7K chainCavPor3.txt.gz 2016-08-15 13:08 655M chainCavPor3Link.sql 2016-08-15 13:10 1.5K chainCavPor3Link.txt.gz 2016-08-15 13:14 2.2G chainHg38.sql 2016-08-15 13:25 1.7K chainHg38.txt.gz 2016-08-15 13:26 608M chainHg38Link.sql 2016-08-15 13:28 1.5K chainHg38Link.txt.gz 2016-08-15 13:31 1.8G chainMm10.sql 2016-08-15 13:39 1.7K chainMm10.txt.gz 2016-08-15 13:39 118M chainMm10Link.sql 2016-08-15 13:39 1.5K chainMm10Link.txt.gz 2016-08-15 13:40 665M chainMm39.sql 2020-11-24 09:08 1.7K chainMm39.txt.gz 2020-11-24 09:08 171M chainMm39Link.sql 2020-11-24 09:14 1.6K chainMm39Link.txt.gz 2020-11-24 09:14 777M chainTupBel1.sql 2016-08-15 13:43 1.7K chainTupBel1.txt.gz 2016-08-15 13:45 1.3G chainTupBel1Link.sql 2016-08-15 13:50 1.5K chainTupBel1Link.txt.gz 2016-08-15 13:55 3.2G chromAlias.sql 2018-02-18 06:37 1.4K chromAlias.txt.gz 2018-02-18 06:37 1.7M chromInfo.sql 2016-08-15 14:09 1.4K chromInfo.txt.gz 2016-08-15 14:09 534K cpgIslandExt.sql 2016-08-15 14:09 1.7K cpgIslandExt.txt.gz 2016-08-15 14:09 1.4M cpgIslandExtUnmasked.sql 2016-08-15 14:09 1.7K cpgIslandExtUnmasked.txt.gz 2016-08-15 14:09 1.6M cytoBandIdeo.sql 2016-08-15 14:09 1.5K cytoBandIdeo.txt.gz 2016-08-15 14:09 519K description.sql 2016-08-15 14:09 1.4K description.txt.gz 2016-08-15 14:09 8.1M development.sql 2016-08-15 14:09 1.4K development.txt.gz 2016-08-15 14:09 47 extFile.sql 2016-08-15 14:09 1.4K extFile.txt.gz 2016-08-15 14:09 80 extNcbiRefSeq.sql 2020-05-10 03:27 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:27 90 gap.sql 2016-08-15 14:09 1.6K gap.txt.gz 2016-08-15 14:09 3.9M gbCdnaInfo.sql 2016-08-15 14:09 2.6K gbCdnaInfo.txt.gz 2016-08-15 14:09 8.8M gbExtFile.sql 2016-08-15 14:09 1.4K gbExtFile.txt.gz 2016-08-15 14:09 1.2K gbLoaded.sql 2020-08-19 10:53 1.6K gbLoaded.txt.gz 2020-08-19 10:53 41K gbMiscDiff.sql 2016-08-15 14:09 1.5K gbMiscDiff.txt.gz 2016-08-15 14:09 4.2K gbSeq.sql 2016-08-15 14:09 1.7K gbSeq.txt.gz 2016-08-15 14:09 11M gbStatus.sql 2016-08-15 14:09 1.9K gbStatus.txt.gz 2016-08-15 14:09 3.2M gbWarn.sql 2016-08-15 14:09 1.3K gbWarn.txt.gz 2016-08-15 14:09 31 gc5BaseBw.sql 2016-08-15 14:09 1.3K gc5BaseBw.txt.gz 2016-08-15 14:09 66 geneName.sql 2016-08-15 14:09 1.4K geneName.txt.gz 2016-08-15 14:09 2.2M genscan.sql 2016-08-15 14:10 1.7K genscan.txt.gz 2016-08-15 14:10 3.5M genscanSubopt.sql 2016-08-15 14:10 1.6K genscanSubopt.txt.gz 2016-08-15 14:10 8.2M gold.sql 2016-08-15 14:10 1.7K gold.txt.gz 2016-08-15 14:10 6.2M grp.sql 2016-08-15 14:10 1.3K grp.txt.gz 2016-08-15 14:10 213 hgFindSpec.sql 2023-12-05 13:51 1.8K hgFindSpec.txt.gz 2023-12-05 13:51 1.0K history.sql 2016-08-15 14:10 1.6K history.txt.gz 2016-08-15 14:10 1.0K imageClone.sql 2016-08-15 14:10 1.5K imageClone.txt.gz 2016-08-15 14:10 35 keyword.sql 2016-08-15 14:10 1.4K keyword.txt.gz 2016-08-15 14:10 561 library.sql 2016-08-15 14:10 1.4K library.txt.gz 2016-08-15 14:10 43 microsat.sql 2016-08-15 14:10 1.5K microsat.txt.gz 2016-08-15 14:10 412K mrnaClone.sql 2016-08-15 14:10 1.4K mrnaClone.txt.gz 2016-08-15 14:10 1.3K multiz5way.sql 2016-08-15 14:10 1.5K multiz5way.txt.gz 2016-08-15 14:10 142M multiz5wayFrames.sql 2016-08-15 14:10 1.7K multiz5wayFrames.txt.gz 2016-08-15 14:10 8.9M multiz5waySummary.sql 2016-08-15 14:10 1.6K multiz5waySummary.txt.gz 2016-08-15 14:10 842K ncbiRefSeq.sql 2020-05-10 03:27 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:27 2.3M ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 208K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 328 ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.0M ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 6.6M ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 2.3M ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.6M nestedRepeats.sql 2016-08-15 14:11 1.9K nestedRepeats.txt.gz 2016-08-15 14:11 15M netCavPor3.sql 2016-08-15 14:11 2.1K netCavPor3.txt.gz 2016-08-15 14:11 97M netHg38.sql 2016-08-15 14:11 2.1K netHg38.txt.gz 2016-08-15 14:11 75M netMm10.sql 2016-08-15 14:12 2.1K netMm10.txt.gz 2016-08-15 14:12 85M netMm39.sql 2020-11-24 09:19 2.1K netMm39.txt.gz 2020-11-24 09:19 85M netTupBel1.sql 2016-08-15 14:12 2.1K netTupBel1.txt.gz 2016-08-15 14:12 79M organism.sql 2016-08-15 14:13 1.4K organism.txt.gz 2016-08-15 14:13 264K phastCons5way.sql 2016-08-15 14:13 1.8K phastCons5way.txt.gz 2016-08-15 14:13 73M phastConsElements5way.sql 2016-08-15 14:13 1.6K phastConsElements5way.txt.gz 2016-08-15 14:13 9.2M phyloP5way.sql 2016-08-15 14:13 1.8K phyloP5way.txt.gz 2016-08-15 14:13 75M productName.sql 2016-08-15 14:14 1.4K productName.txt.gz 2016-08-15 14:14 2.6M refLink.sql 2016-08-15 14:14 1.7K refLink.txt.gz 2016-08-15 14:14 10M refSeqStatus.sql 2016-08-15 14:14 1.6K refSeqStatus.txt.gz 2016-08-15 14:14 1.4M refSeqSummary.sql 2016-08-15 14:14 1.5K refSeqSummary.txt.gz 2016-08-15 14:14 4.7M rmsk.sql 2016-08-15 14:14 1.9K rmsk.txt.gz 2016-08-15 14:14 130M seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 518K sex.sql 2016-08-15 14:15 1.4K sex.txt.gz 2016-08-15 14:15 39 simpleRepeat.sql 2016-08-15 14:15 1.9K simpleRepeat.txt.gz 2016-08-15 14:15 32M source.sql 2016-08-15 14:15 1.4K source.txt.gz 2016-08-15 14:15 269K tableDescriptions.sql 2024-08-31 02:03 1.4K tableDescriptions.txt.gz 2024-08-31 02:03 8.3K tableList.sql 2024-09-01 03:12 1.6K tableList.txt.gz 2024-09-01 03:12 4.3K tissue.sql 2016-08-15 14:15 1.4K tissue.txt.gz 2016-08-15 14:15 132 trackDb.sql 2023-12-05 13:51 2.1K trackDb.txt.gz 2023-12-05 13:51 38K ucscToINSDC.sql 2016-08-15 14:15 1.4K ucscToINSDC.txt.gz 2016-08-15 14:15 957K ucscToRefSeq.sql 2018-02-18 06:37 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:37 918K windowmaskerSdust.sql 2016-08-15 14:15 1.5K windowmaskerSdust.txt.gz 2016-08-15 14:15 165M xenoRefFlat.sql 2020-08-19 10:53 1.7K xenoRefFlat.txt.gz 2020-08-19 10:53 38M xenoRefGene.sql 2020-08-19 10:53 2.0K xenoRefGene.txt.gz 2020-08-19 10:53 41M xenoRefSeqAli.sql 2020-08-19 10:53 2.1K xenoRefSeqAli.txt.gz 2020-08-19 10:53 44M