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