This directory contains a dump of the UCSC genome annotation database for the Sierra Leone 2014 (G3683/KM034562.1/eboVir3) assembly of the Ebola virus 2014 genome (eboVir3, West Africa 01 June 2014 EBOV/G3683/KM034562.1) . 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/4887 http://www.ncbi.nlm.nih.gov/genome/assembly/KM034561 http://www.ncbi.nlm.nih.gov/bioproject/257197 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=eboVir3 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/eboVir3/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/eboVir3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/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 eboVir3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql eboVir3 --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 - bigFiles.sql 2024-12-01 03:30 1.4K bigFiles.txt.gz 2024-12-01 03:30 590 chromInfo.sql 2014-09-30 15:38 1.4K chromInfo.txt.gz 2014-09-30 15:38 71 cytoBandIdeo.sql 2014-09-30 15:38 1.5K cytoBandIdeo.txt.gz 2014-09-30 15:38 186 extFile.sql 2017-01-01 13:06 1.4K extFile.txt.gz 2017-01-01 13:06 347 gap.sql 2014-09-30 15:38 1.6K gap.txt.gz 2014-09-30 15:38 28 gc5BaseBw.sql 2014-09-30 15:38 1.3K gc5BaseBw.txt.gz 2014-09-30 15:38 66 geneDesc.sql 2014-09-30 15:38 1.3K geneDesc.txt.gz 2014-09-30 15:38 2.9K gire2014.sql 2014-09-30 15:38 1.3K gire2014.txt.gz 2014-09-30 15:38 64 gire2014FixedMissense.sql 2014-09-30 15:38 1.3K gire2014FixedMissense.txt.gz 2014-09-30 15:38 86 gire2014KikwitMissense.sql 2014-09-30 15:38 1.3K gire2014KikwitMissense.txt.gz 2014-09-30 15:38 88 gire2014MayingaMissense.sql 2014-09-30 15:38 1.3K gire2014MayingaMissense.txt.gz 2014-09-30 15:38 90 gire2014Missense.sql 2014-09-30 15:38 1.3K gire2014Missense.txt.gz 2014-09-30 15:38 80 gire2014PolymorphicMissense.sql 2014-09-30 15:38 1.3K gire2014PolymorphicMissense.txt.gz 2014-09-30 15:38 98 gire2014SpecificSnps.sql 2014-09-30 15:38 1.3K gire2014SpecificSnps.txt.gz 2014-09-30 15:38 84 gireIntraHost.sql 2014-09-30 15:38 1.3K gireIntraHost.txt.gz 2014-09-30 15:38 74 gireZebov.sql 2014-09-30 15:38 1.3K gireZebov.txt.gz 2014-09-30 15:38 65 gireZebovMissense.sql 2014-09-30 15:38 1.3K gireZebovMissense.txt.gz 2014-09-30 15:38 81 gold.sql 2014-09-30 15:38 1.7K gold.txt.gz 2014-09-30 15:38 61 grp.sql 2014-09-30 15:38 1.3K grp.txt.gz 2014-09-30 15:38 221 hgFindSpec.sql 2023-03-28 13:48 1.8K hgFindSpec.txt.gz 2023-03-28 13:48 255 history.sql 2014-09-30 15:38 1.6K history.txt.gz 2014-09-30 15:38 682 iedbBcell.sql 2014-10-19 10:44 1.3K iedbBcell.txt.gz 2014-10-19 10:44 69 iedbBcellNeg.sql 2014-10-19 10:44 1.3K iedbBcellNeg.txt.gz 2014-10-19 10:44 75 iedbSupp3.sql 2014-12-21 20:39 1.3K iedbSupp3.txt.gz 2014-12-21 20:39 70 iedbTcellI.sql 2014-10-19 10:44 1.3K iedbTcellI.txt.gz 2014-10-19 10:44 71 iedbTcellII.sql 2014-10-19 10:44 1.3K iedbTcellII.txt.gz 2014-10-19 10:44 73 iedbsupp1A0101.sql 2014-12-21 20:39 1.3K iedbsupp1A0101.txt.gz 2014-12-21 20:39 80 iedbsupp1A0201.sql 2014-12-21 20:39 1.3K iedbsupp1A0201.txt.gz 2014-12-21 20:39 80 iedbsupp1A0203.sql 2014-12-21 20:39 1.3K iedbsupp1A0203.txt.gz 2014-12-21 20:39 80 iedbsupp1A0206.sql 2014-12-21 20:39 1.3K iedbsupp1A0206.txt.gz 2014-12-21 20:39 80 iedbsupp1A0301.sql 2014-12-21 20:39 1.3K iedbsupp1A0301.txt.gz 2014-12-21 20:39 80 iedbsupp1A1101.sql 2014-12-21 20:39 1.3K iedbsupp1A1101.txt.gz 2014-12-21 20:39 80 iedbsupp1A2301.sql 2014-12-21 20:39 1.3K iedbsupp1A2301.txt.gz 2014-12-21 20:39 80 iedbsupp1A2402.sql 2014-12-21 20:39 1.3K iedbsupp1A2402.txt.gz 2014-12-21 20:39 80 iedbsupp1A2601.sql 2014-12-21 20:39 1.3K iedbsupp1A2601.txt.gz 2014-12-21 20:39 80 iedbsupp1A3001.sql 2014-12-21 20:39 1.3K iedbsupp1A3001.txt.gz 2014-12-21 20:39 80 iedbsupp1A3002.sql 2014-12-21 20:39 1.3K iedbsupp1A3002.txt.gz 2014-12-21 20:39 80 iedbsupp1A3101.sql 2014-12-21 20:39 1.3K iedbsupp1A3101.txt.gz 2014-12-21 20:39 80 iedbsupp1A3201.sql 2014-12-21 20:39 1.3K iedbsupp1A3201.txt.gz 2014-12-21 20:39 80 iedbsupp1A3301.sql 2014-12-21 20:39 1.3K iedbsupp1A3301.txt.gz 2014-12-21 20:39 80 iedbsupp1A6801.sql 2014-12-21 20:39 1.3K iedbsupp1A6801.txt.gz 2014-12-21 20:39 80 iedbsupp1A6802.sql 2014-12-21 20:39 1.3K iedbsupp1A6802.txt.gz 2014-12-21 20:39 80 iedbsupp1B0702.sql 2014-12-21 20:39 1.3K iedbsupp1B0702.txt.gz 2014-12-21 20:39 80 iedbsupp1B0801.sql 2014-12-21 20:39 1.3K iedbsupp1B0801.txt.gz 2014-12-21 20:39 80 iedbsupp1B1501.sql 2014-12-21 20:39 1.3K iedbsupp1B1501.txt.gz 2014-12-21 20:39 80 iedbsupp1B3501.sql 2014-12-21 20:39 1.3K iedbsupp1B3501.txt.gz 2014-12-21 20:39 80 iedbsupp1B4001.sql 2014-12-21 20:39 1.3K iedbsupp1B4001.txt.gz 2014-12-21 20:39 80 iedbsupp1B4402.sql 2014-12-21 20:39 1.3K iedbsupp1B4402.txt.gz 2014-12-21 20:39 80 iedbsupp1B4403.sql 2014-12-21 20:39 1.3K iedbsupp1B4403.txt.gz 2014-12-21 20:39 80 iedbsupp1B5101.sql 2014-12-21 20:39 1.3K iedbsupp1B5101.txt.gz 2014-12-21 20:39 80 iedbsupp1B5301.sql 2014-12-21 20:39 1.3K iedbsupp1B5301.txt.gz 2014-12-21 20:39 80 iedbsupp1B5701.sql 2014-12-21 20:39 1.3K iedbsupp1B5701.txt.gz 2014-12-21 20:39 80 iedbsupp1B5801.sql 2014-12-21 20:39 1.3K iedbsupp1B5801.txt.gz 2014-12-21 20:39 80 iedbsupp2A01.sql 2014-12-21 20:39 1.3K iedbsupp2A01.txt.gz 2014-12-21 20:39 76 iedbsupp2A02.sql 2014-12-21 20:39 1.3K iedbsupp2A02.txt.gz 2014-12-21 20:39 76 iedbsupp2A07.sql 2014-12-21 20:39 1.3K iedbsupp2A07.txt.gz 2014-12-21 20:39 76 iedbsupp2A11.sql 2014-12-21 20:39 1.3K iedbsupp2A11.txt.gz 2014-12-21 20:39 76 iedbsupp2A20102.sql 2014-12-21 20:39 1.3K iedbsupp2A20102.txt.gz 2014-12-21 20:39 82 iedbsupp2A70103.sql 2014-12-21 20:39 1.3K iedbsupp2A70103.txt.gz 2014-12-21 20:39 82 iedbsupp2A102201.sql 2014-12-21 20:39 1.3K iedbsupp2A102201.txt.gz 2014-12-21 20:39 84 iedbsupp2A102601.sql 2014-12-21 20:39 1.3K iedbsupp2A102601.txt.gz 2014-12-21 20:39 84 iedbsupp2B00101.sql 2014-12-21 20:39 1.3K iedbsupp2B00101.txt.gz 2014-12-21 20:39 82 iedbsupp2B00301.sql 2014-12-21 20:39 1.3K iedbsupp2B00301.txt.gz 2014-12-21 20:39 82 iedbsupp2B01.sql 2014-12-21 20:39 1.3K iedbsupp2B01.txt.gz 2014-12-21 20:39 76 iedbsupp2B01001.sql 2014-12-21 20:39 1.3K iedbsupp2B01001.txt.gz 2014-12-21 20:39 82 iedbsupp2B03901.sql 2014-12-21 20:39 1.3K iedbsupp2B03901.txt.gz 2014-12-21 20:39 82 iedbsupp2B06601.sql 2014-12-21 20:39 1.3K iedbsupp2B06601.txt.gz 2014-12-21 20:39 82 iedbsupp2B08.sql 2014-12-21 20:39 1.3K iedbsupp2B08.txt.gz 2014-12-21 20:39 76 iedbsupp2B08301.sql 2014-12-21 20:39 1.3K iedbsupp2B08301.txt.gz 2014-12-21 20:39 82 iedbsupp2B08701.sql 2014-12-21 20:39 1.3K iedbsupp2B08701.txt.gz 2014-12-21 20:39 82 iedbsupp2B09001.sql 2014-12-21 20:39 1.3K iedbsupp2B09001.txt.gz 2014-12-21 20:39 82 iedbsupp2B17.sql 2014-12-21 20:39 1.3K iedbsupp2B17.txt.gz 2014-12-21 20:39 76 mafSnp160way.sql 2014-09-30 15:38 1.5K mafSnp160way.txt.gz 2014-09-30 15:38 602K mafSnpStrainName160way.sql 2014-09-30 15:38 1.6K mafSnpStrainName160way.txt.gz 2014-09-30 15:38 675K muPIT.sql 2014-11-02 20:43 1.5K muPIT.txt.gz 2014-11-02 20:43 6.7K multiz160way.sql 2014-09-30 15:38 1.5K multiz160way.txt.gz 2014-09-30 15:38 2.2K multiz160wayFrames.sql 2014-09-30 15:38 1.7K multiz160wayFrames.txt.gz 2014-09-30 15:38 176 ncbiGene.sql 2014-09-30 15:38 1.7K ncbiGene.txt.gz 2014-09-30 15:38 238 ncbiGenePfam.sql 2014-09-30 15:38 1.8K ncbiGenePfam.txt.gz 2014-09-30 15:38 493 newSequences.sql 2015-02-24 15:04 1.5K newSequences.txt.gz 2015-02-24 15:04 169 newSequencesFrames.sql 2015-02-24 15:04 1.7K newSequencesFrames.txt.gz 2015-02-24 15:04 3.8K newSequencesSnpView.sql 2015-02-24 15:04 1.6K newSequencesSnpView.txt.gz 2015-02-24 15:04 47K patBulk.sql 2016-04-10 03:26 1.3K patBulk.txt.gz 2016-04-10 03:26 61 patNonBulk.sql 2016-04-10 03:26 1.3K patNonBulk.txt.gz 2016-04-10 03:26 67 pdb.sql 2014-09-30 15:38 1.8K pdb.txt.gz 2014-09-30 15:38 880 phastCons160way.sql 2014-11-02 20:43 1.8K phastCons160way.txt.gz 2014-11-02 20:43 567 phastConsElements160way.sql 2014-11-02 20:43 1.6K phastConsElements160way.txt.gz 2014-11-02 20:43 1.4K phyloP160way.sql 2014-11-02 20:43 1.8K phyloP160way.txt.gz 2014-11-02 20:43 685 spAnnot.sql 2014-10-19 10:44 1.3K spAnnot.txt.gz 2014-10-19 10:44 61 spMut.sql 2014-10-19 10:44 1.3K spMut.txt.gz 2014-10-19 10:44 57 spStruct.sql 2014-10-19 10:44 1.3K spStruct.txt.gz 2014-10-19 10:44 63 strainName160way.sql 2014-09-30 15:38 1.5K strainName160way.txt.gz 2014-09-30 15:38 2.2K strainName160wayFrames.sql 2014-09-30 15:38 1.8K strainName160wayFrames.txt.gz 2014-09-30 15:38 180 strainPhastCons160way.sql 2014-11-02 20:43 1.8K strainPhastCons160way.txt.gz 2014-11-02 20:43 573 strainPhastConsElements160way.sql 2014-11-02 20:43 1.6K strainPhastConsElements160way.txt.gz 2014-11-02 20:43 1.4K strainPhyloP160way.sql 2014-11-02 20:43 1.8K strainPhyloP160way.txt.gz 2014-11-02 20:43 691 tableDescriptions.sql 2024-11-30 02:03 1.5K tableDescriptions.txt.gz 2024-11-30 02:03 3.4K tableList.sql 2024-12-01 03:30 1.6K tableList.txt.gz 2024-12-01 03:30 1.9K trackDb.sql 2023-03-28 13:48 2.1K trackDb.txt.gz 2023-03-28 13:48 37K