This directory contains the Nov. 2004 update of the rat genome (rn4, Nov. 2004, version 3.4) from the Rat Genome Sequencing Consortium. The assembly was produced at the Baylor College of Medicine Human Genome Seuqencing Center. For more information on the rat genome, see the Rat Genome Project website for the Baylor College of Medicine Human Genome Sequencing Center at http://www.hgsc.bcm.tmc.edu/. Files included in this directory: chromAgp.tar.gz - Description of how the working draft was generated from fragments at a chromosome layout level. chromFa.tar.gz - The working draft sequence chromosome in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are in lower case while non-repeating sequence is in upper case. chromFaMasked.tar.gz - The working draft sequence chromosome in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. rn4.2bit - rn4.2bit contains the complete rn4 Rat Genome in the 2bit format. A utility program, twoBitToFa (available from our src tree), can be used to extract .fa file(s) from this file. chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were done with RepeatMasker at the -s sensitive setting. The full set of arguments used for the RepeatMasker operation were: -ali -s -spec rat -comp mouse chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, translated into one .bed file per chromosomes. est.fa.gz - Rat ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. rn4.quals.fa.gz - quality scores in fasta file format md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - Rat 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.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. rn4.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 goldenPath/rn4/bigZips. To download multiple files, use hgdownload.cse.ucsc.edu, then go to the directory the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) These data are made available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (the Rat Genome Sequencing Consortium) are properly acknowledged. 3. The Centers producing the data reserve the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects (see http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537). 5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2006-01-30 15:37 3.6M chromFa.tar.gz 2006-03-17 10:00 807M chromFaMasked.tar.gz 2006-03-17 10:08 473M chromOut.tar.gz 2006-03-17 09:47 137M chromTrf.tar.gz 2006-01-30 15:58 15M est.fa.gz 2020-02-28 18:43 208M est.fa.gz.md5 2020-02-28 18:43 44 md5sum.txt 2010-01-04 14:56 347 mrna.fa.gz 2020-02-28 18:28 25M mrna.fa.gz.md5 2020-02-28 18:28 45 refMrna.fa.gz 2020-02-28 18:44 15M refMrna.fa.gz.md5 2020-02-28 18:44 48 rn4.2bit 2006-03-17 09:36 710M rn4.chrom.sizes 2006-01-30 15:18 789 rn4.fa.gz 2020-01-23 02:26 807M rn4.quals.fa.gz 2009-06-09 12:13 346M upstream1000.fa.gz 2020-02-28 18:45 4.2M upstream1000.fa.gz.md5 2020-02-28 18:45 53 upstream2000.fa.gz 2020-02-28 18:45 8.1M upstream2000.fa.gz.md5 2020-02-28 18:45 53 upstream5000.fa.gz 2020-02-28 18:45 19M upstream5000.fa.gz.md5 2020-02-28 18:45 53 xenoMrna.fa.gz 2020-02-28 18:37 6.8G xenoMrna.fa.gz.md5 2020-02-28 18:38 49 xenoRefMrna.fa.gz 2020-02-28 18:44 322M xenoRefMrna.fa.gz.md5 2020-02-28 18:44 52