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 axtTight directory contains relatively stringent
human/mouse alignments filtered so that only the best
alignment for any given region of the human genome
is used.
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 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 human genome while axtBest covers
40%.
Name Last modified Size Description
Parent Directory -
chrY.axt.gz 2003-11-03 16:51 279K
chrX_random.axt.gz 2003-11-03 16:51 94K
chrX.axt.gz 2003-11-03 16:51 6.5M
chrUn_random.axt.gz 2003-11-03 16:51 79K
chrM.axt.gz 2003-11-03 16:51 8.3K
chr22.axt.gz 2003-11-03 16:49 1.2M
chr21.axt.gz 2003-11-03 16:49 973K
chr20.axt.gz 2003-11-03 16:49 2.4M
chr19.axt.gz 2003-11-03 16:48 1.9M
chr18_random.axt.gz 2003-11-03 16:48 212
chr18.axt.gz 2003-11-03 16:48 2.5M
chr17_random.axt.gz 2003-11-03 16:48 49K
chr17.axt.gz 2003-11-03 16:48 4.1M
chr16.axt.gz 2003-11-03 16:47 3.6M
chr15_random.axt.gz 2003-11-03 16:47 36K
chr15.axt.gz 2003-11-03 16:47 3.7M
chr14.axt.gz 2003-11-03 16:47 3.8M
chr13_random.axt.gz 2003-11-03 16:47 10K
chr13.axt.gz 2003-11-03 16:47 3.2M
chr12.axt.gz 2003-11-03 16:46 4.7M
chr11.axt.gz 2003-11-03 16:46 5.5M
chr10_random.axt.gz 2003-11-03 16:46 29K
chr10.axt.gz 2003-11-03 16:46 5.0M
chr9_random.axt.gz 2003-11-03 16:51 73K
chr9.axt.gz 2003-11-03 16:51 4.6M
chr8_random.axt.gz 2003-11-03 16:51 16K
chr8.axt.gz 2003-11-03 16:51 4.7M
chr7_random.axt.gz 2003-11-03 16:51 7.6K
chr7.axt.gz 2003-11-03 16:51 5.7M
chr6_random.axt.gz 2003-11-03 16:50 36K
chr6.axt.gz 2003-11-03 16:50 6.1M
chr5_random.axt.gz 2003-11-03 16:50 3.2K
chr5.axt.gz 2003-11-03 16:50 7.0M
chr4_random.axt.gz 2003-11-03 16:50 13K
chr4.axt.gz 2003-11-03 16:50 6.0M
chr3_random.axt.gz 2003-11-03 16:49 36K
chr3.axt.gz 2003-11-03 16:49 7.9M
chr2_random.axt.gz 2003-11-03 16:49 11K
chr2.axt.gz 2003-11-03 16:48 9.9M
chr1_random.axt.gz 2003-11-03 16:48 161K
chr1.axt.gz 2003-11-03 16:45 9.6M