This directory contain human/mouse alignments made
using the Jun 2003 human assembly (also known as build 34) 
vs. the Oct 2003 mouse assembly (also known as mm4 or NCBI
Mouse Build 32). 

The axtNet subdirectory shows the best mouse/human chain for
every part of the mouse genome. For more information on the
chain and net algorithms, see the Methods section of the
description pages associated with the net and chain tracks.

The 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 human sequence with inserts.  
    Line 3 - contains the mouse 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 human chromosome. The first base is
    numbered 1.
4 - End in human chromosome. The end base is included.
5 - Mouse chromosome.
6 - Start in mouse.
7 - End in mouse.
8 - Mouse strand. If this is '-', the mouse start/end fields are 
    relative to the reverse-complemented mouse 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 Pennsylvania State University (PSU).  
Each chromosome was divided into 10010000 base chunks with 10000 
bases of overlap. The .lav format blastz output, which does not 
include the sequence, was converted to .axt with PSU's lavToAxt.

The axtNet alignments were processed with chainNet, netSyntenic,
and netClass from Jim Kent at UCSC.