This directory contains the Jun. 2003 update of the rat genome 
(rn3, Jun. 2003) 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.zip - Description of how the working draft was generated from
    fragments at a chromosome layout level. 

chromFa.zip - 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.zip - The working draft sequence chromosome 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 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.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per chromosomes.  

contigAgp.zip - Description of how the working draft was generated from
    fragments at a contig layout level. 

contigFa.zip - The working draft sequence contig in one file per
    contig.  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.

contigFaMasked.zip - The working draft sequence contig 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 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

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per contig.  

est.fa.gz - Rat ESTs in GenBank. This sequence data is updated once a 
    week via automatic GenBank updates.

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.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - 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.
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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 goldenPath/rnJun2003/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.