This directory contains alignments of the human assembly (hg17, 
May 2004) to the rat assembly (rn3, Jun. 2003).

Files included in this directory:

  - axtNet directory: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in 
    by next-best chains where possible. 

  - axtTight directory: contains a highly conserved subset of the best 
    alignments for any part of the mouse genome. 

  - human.chain.gz: chained blastz alignments. The chain format is 
    described in http://genome.ucsc.edu/goldenPath/help/chain.html.

  - human.net.gz: "net" file that describes rearrangements between the 
    species and the best human match to any part of the mouse genome.  
    The net format is described in 
    http://genome.ucsc.edu/goldenPath/help/net.html.

  - md5sum.txt: checksums of the files in this directory

The alignments in the axtNet and axtTight directories are in "axt" 
format. For a description, see 
http://genome.ucsc.edu/goldenPath/help/axt.html.

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:

         A    C    G    T
    A   91 -114  -31 -123
    C -114  100 -125  -31
    G  -31 -125  100 -114
    T -123  -31 -114   91

with a gap open penalty of 400 and a gap extension penalty of 30.  The 
minimum score for an alignment to be kept was 5000 for the first pass  
and 2200 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.

Each chromosome was divided into 10,010,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. 

The axtNet alignments were processed with chainNet, netSyntenic,
and netClass written by Jim Kent at UCSC. The axtTight alignments were 
processed with subsetAxt from Jim Kent using the matrix:

         A    C    G    T
    A  100 -200 -100 -200
    C -200  100 -200 -100
    G -100 -200  100 -200
    T -200 -100 -200  100

with a gap open penalty of 2000 and a gap extension penalty of 50. 
The minimum score was 3400. The axtTight subset covers 6% of the rat 
genome while axtBest covers 40%.

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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/rnJun2003/vshg17/. 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 usable for any purpose. 
The rat 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.