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.
Name Last modified Size Description
Parent Directory -
chr1.axt.gz 2003-11-03 15:51 62M
chr10.axt.gz 2003-11-03 15:53 36M
chr10_random.axt.gz 2003-11-03 15:53 221K
chr11.axt.gz 2003-11-03 15:54 35M
chr12.axt.gz 2003-11-03 15:56 33M
chr13.axt.gz 2003-11-03 15:57 24M
chr13_random.axt.gz 2003-11-03 15:57 50K
chr14.axt.gz 2003-11-03 15:58 25M
chr15.axt.gz 2003-11-03 15:58 23M
chr15_random.axt.gz 2003-11-03 15:58 230K
chr16.axt.gz 2003-11-03 15:59 22M
chr17.axt.gz 2003-11-03 16:00 23M
chr17_random.axt.gz 2003-11-03 16:00 337K
chr18.axt.gz 2003-11-03 16:01 19M
chr18_random.axt.gz 2003-11-03 16:01 1.8K
chr19.axt.gz 2003-11-03 16:03 8.8M
chr1_random.axt.gz 2003-11-03 16:03 1.0M
chr2.axt.gz 2003-11-03 16:06 66M
chr20.axt.gz 2003-11-03 16:06 17M
chr21.axt.gz 2003-11-03 16:07 7.8M
chr22.axt.gz 2003-11-03 16:07 8.0M
chr2_random.axt.gz 2003-11-03 16:07 81K
chr3.axt.gz 2003-11-03 16:09 55M
chr3_random.axt.gz 2003-11-03 16:09 215K
chr4.axt.gz 2003-11-03 16:11 46M
chr4_random.axt.gz 2003-11-03 16:11 80K
chr5.axt.gz 2003-11-03 16:13 48M
chr5_random.axt.gz 2003-11-03 16:13 18K
chr6.axt.gz 2003-11-03 16:15 45M
chr6_random.axt.gz 2003-11-03 16:15 410K
chr7.axt.gz 2003-11-03 16:16 40M
chr7_random.axt.gz 2003-11-03 16:16 61K
chr8.axt.gz 2003-11-03 16:18 36M
chr8_random.axt.gz 2003-11-03 16:18 120K
chr9.axt.gz 2003-11-03 16:20 31M
chr9_random.axt.gz 2003-11-03 16:20 387K
chrM.axt.gz 2003-11-03 16:20 9.5K
chrUn_random.axt.gz 2003-11-03 16:20 543K
chrX.axt.gz 2003-11-03 16:22 31M
chrX_random.axt.gz 2003-11-03 16:22 444K
chrY.axt.gz 2003-11-03 16:22 1.8M