This directory contains the Jan. 2003 update of the rat genome
(rn2, Jan. 2003) from the Rat Genome Sequencing Consortium. The
assembly was produced at the Baylor College of Medicine Human Genome
Sequencing Center. For more information on the rat genome, see the
Baylor Rat Genome Project website at http://www.hgsc.bcm.tmc.edu/.
Files included in this directory:
chromAgp.zip - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.zip - 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 June 2003 version with RepBase
libraries: RepBase Update 8.4, RM database version 20030619
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 of less than or equal to 12, and translated
into one .bed file per chromosome.
contigAgp.zip - Description of how the assembly was generated from
fragments at a contig layout level.
contigFa.zip - The assembly sequence contig, in one file per contig.
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.
contigFaMasked.zip - The assembly sequence contigs, in one file
per contig. Repeats are masked by capital Ns; non-repeating sequence
is shown in upper case.
contigOut.zip - RepeatMasker .out file for contigs. These were
created by RepeatMasker at the -s sensitive setting.
contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into one .bed
file per contig.
mrna.zip - Mouse mRNA from GenBank.
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.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
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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/rnJan2003/bigZips. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the files in this directory are freely available for any use.
Name Last modified Size Description
Parent Directory -
chromAgp.zip 2003-03-06 11:25 3.3M
chromFa.zip 2003-03-06 12:06 785M
chromFaMasked.zip 2003-03-06 12:29 461M
chromOut.zip 2003-03-06 11:28 132M
chromTrf.zip 2003-03-06 13:35 14M
contigAgp.zip 2003-03-06 12:29 3.4M
contigFa.zip 2003-03-06 13:10 785M
contigFaMasked.zip 2003-03-06 13:34 462M
contigOut.zip 2003-03-06 12:32 131M
contigTrf.zip 2003-03-06 13:35 15M
mrna.zip 2003-05-06 16:45 4.6M
upstream1000.zip 2003-05-09 22:47 1.0M
upstream2000.zip 2003-05-09 22:47 2.0M
upstream5000.zip 2003-05-09 22:48 4.7M