This directory contains the June 2004 Zv4 assembly of the zebrafish genome (UCSC version 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. Files included in this directory: - chr*.fa.zip: compressed FASTA sequence of each chromosome. Repeats (from RepeatMasker and Tandem Repeat Finder) are in lower case while non-repeating sequence is 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. - md5sum.txt - Checksum file. NOTE: chr1.fa.zip was replaced with chr1New.fa.zip on 06/06/05 because chr1.fa was found to be incompletely repeat-masked. This problem has been corrected in chr1New.fa.zip. 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. ------------------------------------------------------------------ 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/chromosomes. 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 - chr1.fa.zip 2004-12-14 09:12 17M chr1New.fa.zip 2005-06-06 19:22 18M chr2.fa.zip 2004-12-14 09:18 16M chr3.fa.zip 2004-12-14 09:22 13M chr4.fa.zip 2004-12-14 09:22 10M chr5.fa.zip 2004-12-14 09:23 20M chr6.fa.zip 2004-12-14 09:23 9.9M chr7.fa.zip 2004-12-14 09:24 19M chr8.fa.zip 2004-12-14 09:25 11M chr9.fa.zip 2004-12-14 09:25 13M chr10.fa.zip 2004-12-14 09:12 11M chr11.fa.zip 2004-12-14 09:13 11M chr12.fa.zip 2004-12-14 09:13 10M chr13.fa.zip 2004-12-14 09:14 11M chr14.fa.zip 2004-12-14 09:14 18M chr15.fa.zip 2004-12-14 09:15 11M chr16.fa.zip 2004-12-14 09:15 13M chr17.fa.zip 2004-12-14 09:16 13M chr18.fa.zip 2004-12-14 09:17 14M chr19.fa.zip 2004-12-14 09:17 15M chr20.fa.zip 2004-12-14 09:19 18M chr21.fa.zip 2004-12-14 09:19 12M chr22.fa.zip 2004-12-14 09:20 11M chr23.fa.zip 2004-12-14 09:20 13M chr24.fa.zip 2004-12-14 09:21 7.6M chr25.fa.zip 2004-12-14 09:21 7.7M chrM.fa.zip 2004-12-14 09:25 5.5K chrNA.fa.zip 2004-12-14 09:29 89M chrUn.fa.zip 2004-12-14 09:31 51M md5sum.txt 2005-06-06 19:24 1.3K