These directories contain mouse/rat alignments made
using the Feb. 2002 mouse assembly (also known as MGSCv3, mm2)
vs. the Nov. 2002 rat assembly (also known as rn1). 

The directories are:

    axtBest - contains alignments filtered so that only
              the best alignment for any given region
	      of the mouse genome is left.
    axtTight - contains only a relatively stringent
               subset of the axtBest alignments.

All alignments are in 'axt' format.   Each alignment
contains three lines and is separated from the next
alignment by a space:   

    Line 1 - summarizes the alignment.   
    Line 2 - contains the mouse sequence with inserts.  
    Line 3 - contains the rat sequence with inserts.  

The summary line contains 9 blank separated fields with the 
following meanings:

1 - Alignment number.  The first alignment in a file
    is numbered 0,  the next 1, and so forth.
2 - Human chromosome.
3 - Start in mouse chromosome.  The first base is
    numbered 1.
4 - End in mouse chromosome.  The end base is included.
5 - Rat chromosome.
6 - Start in rat.
7 - End in rat.
8 - Rat strand.   If this is '-' then the rat start/
    rat end fields are relative to the reverse complemented
    rat chromosome.
9 - Blastz score.   The scoring matrix blastz uses is:

           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 3000 for the first pass,  and then
    2200 for the second pass, which just restricts
    the search space to the regions between two alignments
    found in the first pass.

The alignments were done with blastz, which is available
from Webb Miller's group at PSU.  Each chromosome
was divided into 10010000 base chunks with 10000 bases
of overlap.  The axtAll alignments include this overlap.
The .lav format blastz output, which does not include
the sequence, was converted to .axt with PSU's lav2axt.
The axtBest alignments were processed with axtBest from
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 rat genome data has specific conditions for use. Please 
refer to http://genome.ucsc.edu/goldenPath/credits.html for 
details.