This directory contain human/rat alignments made
using the July 2003 human assembly (also known as build 34) 
vs. the June 2003 rat assembly (also known as rn3). 

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 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 human chromosome. The first base is
    numbered 1.
4 - End in human chromosome. The end base is included.
5 - Rat chromosome.
6 - Start in rat.
7 - End in rat.
8 - Rat strand. If this is '-', the rat start/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 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.  
      Name                    Last modified      Size  Description
Parent Directory - chrY.axt.gz 2003-08-25 17:44 1.8M chrX_random.axt.gz 2003-08-25 17:44 448K chrX.axt.gz 2003-08-25 17:43 31M chrUn_random.axt.gz 2003-08-25 17:43 576K chrM.axt.gz 2003-08-25 17:43 10K chr9_random.axt.gz 2003-08-25 17:43 380K chr9.axt.gz 2003-08-25 17:42 31M chr8_random.axt.gz 2003-08-25 17:42 131K chr8.axt.gz 2003-08-25 17:42 37M chr7_random.axt.gz 2003-08-25 17:41 58K chr7.axt.gz 2003-08-25 17:41 40M chr6_random.axt.gz 2003-08-25 17:40 410K chr6.axt.gz 2003-08-25 17:40 44M chr5_random.axt.gz 2003-08-25 17:39 20K chr5.axt.gz 2003-08-25 17:39 49M chr4_random.axt.gz 2003-08-25 17:38 76K chr4.axt.gz 2003-08-25 17:38 47M chr3_random.axt.gz 2003-08-25 17:36 223K chr3.axt.gz 2003-08-25 17:36 55M chr2_random.axt.gz 2003-08-25 17:35 95K chr22.axt.gz 2003-08-25 17:35 8.0M chr21.axt.gz 2003-08-25 17:35 7.6M chr20.axt.gz 2003-08-25 17:35 16M chr2.axt.gz 2003-08-25 17:34 65M chr1_random.axt.gz 2003-08-25 17:33 1.1M chr19.axt.gz 2003-08-25 17:33 9.2M chr18_random.axt.gz 2003-08-25 17:32 833 chr18.axt.gz 2003-08-25 17:32 19M chr17_random.axt.gz 2003-08-25 17:32 269K chr17.axt.gz 2003-08-25 17:32 22M chr16.axt.gz 2003-08-25 17:31 21M chr15_random.axt.gz 2003-08-25 17:31 228K chr15.axt.gz 2003-08-25 17:31 24M chr14.axt.gz 2003-08-25 17:30 24M chr13_random.axt.gz 2003-08-25 17:30 43K chr13.axt.gz 2003-08-25 17:30 23M chr12.axt.gz 2003-08-25 17:29 33M chr11.axt.gz 2003-08-25 17:28 37M chr10_random.axt.gz 2003-08-25 17:27 222K chr10.axt.gz 2003-08-25 17:27 36M chr1.axt.gz 2003-08-25 17:26 60M