This directory contains the June 2004 Zv4 freeze of the zebrafish genome (danRer2) 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. NOTE: chr1.fa in chromFa.zip and chr1.fa.masked in chromFaMasked.zip were replaced with chr1New.fa and chr1New.fa.masked, respectively, on 06/06/05 because the original chr1.fa was found to be incompletely repeat-masked. This problem has been corrected in chr1New.fa.zip, found in the danRer2/chromosomes directory. chromOut.zip contains a new chr1New.fa.out RepeatMasker file in which an erroneous line in the output has been removed. The Blastz alignments, Human Proteins tBLASTn and the Blat alignments of the ESTs, mRNAs, Affymetrix probe consensus sequences, BAC ends and Radiation Hybrid Map sequences were all created using the incompletely masked chromosome 1. Files included in this directory: chromAgp.zip - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.zip - [See NOTE above] 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 9.04, RM database version 20040702 with the addition of the zebunc.ref (Zebrafish Unclassified) repeats library from RepBase 9.06. chromFaMasked.zip - [See NOTE above] The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - [See NOTE above] 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. upstream1000.zip - Sequences 1000 bases upstream of annotated transcription start of RefSeq genes. This includes only the cases where the transcription start is annotated separately from the coding region start. Note that upstream files are generated only when an assembly is released. Therefore, the data may be slightly out of synch with the RefSeq data in assemblies that are incrementally updated nightly. 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. danRer2.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/danRer2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The Zv4 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/Zv4release/. 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.zip 2005-04-25 10:25 492K chromFa.zip 2005-06-06 18:55 466M chromFaMasked.zip 2005-06-06 19:15 264M chromOut.zip 2005-06-06 18:48 110M chromTrf.zip 2004-12-14 09:03 7.9M danRer2.chrom.sizes 2004-12-02 14:53 409 est.fa.gz 2008-09-10 17:30 289M md5sum.txt 2005-06-06 19:23 519 mrna.fa.gz 2008-09-10 17:07 16M refMrna.fa.gz 2008-09-10 17:31 9.4M upstream1000.zip 2004-12-14 09:04 1.3M upstream2000.zip 2004-12-14 09:05 2.5M xenoMrna.fa.gz 2008-09-10 17:12 686M