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
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
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
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
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
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
1. The data may be freely downloaded, used in analyses, and repackaged
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
5. Any redistribution of the data should carry this notice.
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