This directory contains the May 2005 Zv5 freeze of the zebrafish genome (danRer3) obtained from the Wellcome Trust Sanger Institute and 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. Files included in this directory: danRer3.2bit - contains the complete zebrafish/danRer3 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 chromAgp.tar.gz - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.tar.gz - The assembly sequence in one file per chromosome. 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. RepeatMasker open-3.0 version with RepBase libraries: RepBase Update 9.11, RM database version 20050112 with the addition of the zebunc.ref (Zebrafish Unclassified) repeats library from RepBase 10.04. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per chromosomes. est.fa.gz - Zebrafish ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. 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. scaffoldUnsFa.tar.gz - Individual scaffold sequences with one file for each of chrUn and chrNA scaffolds. Masking is the same as for chromFa.tar.gz. Repeats are shown in lower case; non-repeating sequence is shown in upper case. scaffoldUnsFaMasked.tar.gz - Individual scaffold sequences with one file for each of chrUn and chrNA scaffolds. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. 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.zip - Same as upstream1000, but 2000 bases. upstream5000.zip - 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. danRer3.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 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/danRer3/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The Zv5 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/Zv5release/. 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 - chromAgp.tar.gz 2005-08-04 11:24 375K chromFa.tar.gz 2005-08-04 11:32 493M chromFaMasked.tar.gz 2005-08-04 11:38 272M chromOut.tar.gz 2005-08-04 11:25 117M chromTrf.tar.gz 2005-08-04 11:39 8.9M danRer3.2bit 2005-06-15 17:13 416M danRer3.chrom.sizes 2005-06-16 14:07 409 danRer3.fa.gz 2020-01-23 02:20 494M est.fa.gz 2020-02-27 22:52 305M est.fa.gz.md5 2020-02-27 22:52 44 md5sum.txt 2014-02-03 11:34 417 mrna.fa.gz 2020-02-27 22:46 18M mrna.fa.gz.md5 2020-02-27 22:46 45 refMrna.fa.gz 2020-02-27 22:52 12M refMrna.fa.gz.md5 2020-02-27 22:52 48 scaffoldUnsFa.tar.gz 2005-08-04 11:34 125M scaffoldUnsFaMasked.tar.gz 2005-08-04 11:39 66M upstream1000.fa.gz 2020-02-27 22:53 3.9M upstream1000.fa.gz.md5 2020-02-27 22:53 53 upstream2000.fa.gz 2020-02-27 22:53 7.5M upstream2000.fa.gz.md5 2020-02-27 22:53 53 upstream5000.fa.gz 2020-02-27 22:54 18M upstream5000.fa.gz.md5 2020-02-27 22:54 53 xenoMrna.fa.gz 2016-03-14 08:38 5.0G xenoMrna.fa.gz.md5 2016-03-14 08:38 49 xenoRefMrna.fa.gz 2020-02-27 22:52 325M xenoRefMrna.fa.gz.md5 2020-02-27 22:52 52