This directory contain human/rat alignments made
using the May 2004 human assembly (also known as
NCBI build 35, UCSC build hg17) vs. the June 2003
rat assembly (also known as UCSC build 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 -
chr1.axt.gz 16-Aug-2005 14:28 59M
chr1_random.axt.gz 16-Aug-2005 14:28 757K
chr2.axt.gz 16-Aug-2005 14:31 64M
chr2_random.axt.gz 16-Aug-2005 14:31 41K
chr3.axt.gz 16-Aug-2005 14:32 54M
chr3_random.axt.gz 16-Aug-2005 14:32 263K
chr4.axt.gz 16-Aug-2005 14:33 46M
chr4_random.axt.gz 16-Aug-2005 14:33 126K
chr5.axt.gz 23-Nov-2005 15:48 48M
chr5_random.axt.gz 16-Aug-2005 14:35 19K
chr6.axt.gz 16-Aug-2005 14:35 43M
chr6_hla_hap1.axt.gz 16-Aug-2005 14:35 16K
chr6_hla_hap2.axt.gz 16-Aug-2005 14:35 15K
chr6_random.axt.gz 16-Aug-2005 14:35 396K
chr7.axt.gz 16-Aug-2005 14:36 39M
chr7_random.axt.gz 16-Aug-2005 14:36 65K
chr8.axt.gz 16-Aug-2005 14:37 36M
chr8_random.axt.gz 16-Aug-2005 14:37 83K
chr9.axt.gz 16-Aug-2005 14:38 31M
chr9_random.axt.gz 16-Aug-2005 14:38 93K
chr10.axt.gz 16-Aug-2005 14:19 36M
chr10_random.axt.gz 16-Aug-2005 14:19 17K
chr11.axt.gz 16-Aug-2005 14:21 36M
chr12.axt.gz 16-Aug-2005 14:22 32M
chr12_random.axt.gz 16-Aug-2005 14:22 75K
chr13.axt.gz 16-Aug-2005 14:23 23M
chr13_random.axt.gz 16-Aug-2005 14:23 40K
chr14.axt.gz 16-Aug-2005 14:24 24M
chr15.axt.gz 16-Aug-2005 14:25 23M
chr15_random.axt.gz 16-Aug-2005 14:25 187K
chr16.axt.gz 16-Aug-2005 14:25 21M
chr16_random.axt.gz 16-Aug-2005 14:25 14K
chr17.axt.gz 16-Aug-2005 14:26 22M
chr17_random.axt.gz 16-Aug-2005 14:26 282K
chr18.axt.gz 16-Aug-2005 14:26 19M
chr18_random.axt.gz 16-Aug-2005 14:26 806
chr19.axt.gz 16-Aug-2005 14:27 9.0M
chr19_random.axt.gz 16-Aug-2005 14:27 29K
chr20.axt.gz 16-Aug-2005 14:29 16M
chr21.axt.gz 16-Aug-2005 14:29 7.5M
chr22.axt.gz 16-Aug-2005 14:30 7.9M
chr22_random.axt.gz 16-Aug-2005 14:30 49K
chrM.axt.gz 16-Aug-2005 14:38 10K
chrX.axt.gz 16-Aug-2005 14:38 31M
chrX_random.axt.gz 16-Aug-2005 14:39 169K
chrY.axt.gz 16-Aug-2005 14:39 1.8M
md5sum.txt 17-Jan-2006 14:07 2.2K