This directory contains the Jul. 2007 Zv7 assembly of the zebrafish genome (danRer5) obtained from the Wellcome Trust Sanger Institute, as well as repeat annotations and GenBank sequences. This assembly was produced by a collaboration between the Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute for Developmental Biology in Tuebingen, Germany, the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands and Yi Zhou and Leonard Zon from the Children's Hospital in Boston, Massachusetts. For more information on the zebrafish genome, see the project website: http://www.sanger.ac.uk/Projects/D_rerio/ Files included in this directory: danRer5.2bit - contains the complete zebrafish/danRer5 genome sequence in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. The utility program, twoBitToFa (available from the kent src tree), can be used to extract .fa file(s) from this file. A pre-compiled version of the command line tool can be found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html danRer5.agp.gz - Description of how the assembly was generated from fragments. danRer5.fa.gz - "Soft-masked" assembly sequence in one file. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. danRer5.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. danRer5.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. May 17 2007 (open-3-1-8) version of RepeatMasker with the RepeatMasker library RELEASE 20061006. The RepeatMasker library included the addition of repeats from the zebunc.ref (Zebrafish Unclassified) repeats library from RepBase12.07 from the Genetic Information Research Institute (GIRI). Some repeats were removed from zebunc.ref because they mask out real genes (see the danRer5 RepeatMasker track description page for more details). danRer5.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED format. est.fa.gz - Zebrafish ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - checksums of files in this directory mrna.fa.gz - Zebrafish mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. upstream5000.fa.gz - Same as upstream1000, but 5000 bases. xenoMrna.fa.gz - GenBank mRNAs from species other than that of the genome. This sequence data is updated once a week via automatic GenBank updates. danRer5.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------------ If you plan to download a large file or multiple files from this directory, we recommend that 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/danRer5/bigZips. 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/danRer5/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf <file>.tar.gz To uncompress the fa.gz files: gunzip <file>.fa.gz The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained directly from ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence data are made available before scientific publication with the understanding that the groups involved in generating the data intend to publish the initial large-scale analyses of the dataset. This will include a summary detailing the data that have beeen generated and key features of the genome identified from genomic assembly and clone mapping/sequencing. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - danRer5.2bit 2007-09-05 08:54 364M danRer5.agp.gz 2007-09-11 22:03 101K danRer5.chrom.sizes 2007-08-24 15:00 81K danRer5.fa.gz 2007-09-11 22:11 443M danRer5.fa.masked.gz 2007-09-11 22:15 242M danRer5.fa.out.gz 2007-09-11 22:03 105M danRer5.trf.bed.gz 2007-09-11 22:04 8.8M est.fa.gz 2019-10-17 00:07 305M est.fa.gz.md5 2019-10-17 00:07 44 genes/ 2020-02-05 13:46 - md5sum.txt 2014-01-03 15:15 304 mrna.fa.gz 2019-10-17 00:01 18M mrna.fa.gz.md5 2019-10-17 00:01 45 refMrna.fa.gz 2019-10-17 00:07 12M refMrna.fa.gz.md5 2019-10-17 00:07 48 upstream1000.fa.gz 2019-10-17 00:08 4.1M upstream1000.fa.gz.md5 2019-10-17 00:08 53 upstream2000.fa.gz 2019-10-17 00:08 7.8M upstream2000.fa.gz.md5 2019-10-17 00:08 53 upstream5000.fa.gz 2019-10-17 00:08 19M upstream5000.fa.gz.md5 2019-10-17 00:08 53 xenoMrna.fa.gz 2016-03-14 05:17 5.0G xenoMrna.fa.gz.md5 2016-03-14 05:17 49 xenoRefMrna.fa.gz 2019-10-17 00:07 319M xenoRefMrna.fa.gz.md5 2019-10-17 00:07 52