This directory contain chimpanzee/human alignments made
using the Nov 2003 Arachne chimp assembly
(NCBI Build 1 Version 1, UCSC panTro1)
vs. the Human July 2003 human assembly
(NCBI Human Build 34, UCSC hg16).
The axtNet directory contains alignments indicating the best chimp/human chain for
every part of the human genome. For more information on the algorithms used
to generate these alignments, see the Methods section of the
Human Chain and Human Net tracks in the chimpanzee browser.
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 - Target (chimpanzee) chromosome.
3 - Start in target (chimp) chromosome. The first base is
numbered 1.
4 - End in target (chimp) chromosome. The end base is included.
5 - Query (human) chromosome.
6 - Start in query (human).
7 - End in query (human).
8 - Query (human) strand. If this is '-', the query start/end fields are
relative to the reverse-complemented query chromosome.
9 - score.
Name Last modified Size Description
Parent Directory -
md5sum.txt 2004-02-25 10:03 2.5K
chrY_random.axt.gz 2004-02-24 22:58 1.0M
chrY.axt.gz 2004-02-24 22:58 3.0M
chrX_random.axt.gz 2004-02-24 22:58 4.3M
chrX.axt.gz 2004-02-24 22:58 47M
chrUn_random.axt.gz 2004-02-24 22:58 39M
chrM.axt.gz 2004-02-24 22:58 820
chr23_random.axt.gz 2004-02-24 22:58 1.3M
chr23.axt.gz 2004-02-24 22:58 15M
chr22_random.axt.gz 2004-02-24 22:58 1.0M
chr22.axt.gz 2004-02-24 22:58 17M
chr21_random.axt.gz 2004-02-24 22:58 2.0M
chr21.axt.gz 2004-02-24 22:58 30M
chr20_random.axt.gz 2004-02-24 22:58 2.2M
chr20.axt.gz 2004-02-24 22:58 24M
chr19_random.axt.gz 2004-02-24 22:58 15M
chr19.axt.gz 2004-02-24 22:58 26M
chr18_random.axt.gz 2004-02-24 22:58 3.5M
chr18.axt.gz 2004-02-24 22:58 35M
chr17_random.axt.gz 2004-02-24 22:58 4.6M
chr17.axt.gz 2004-02-24 22:58 37M
chr16_random.axt.gz 2004-02-24 22:58 5.1M
chr16.axt.gz 2004-02-24 22:58 38M
chr15_random.axt.gz 2004-02-24 22:58 1.8M
chr15.axt.gz 2004-02-24 22:58 33M
chr14_random.axt.gz 2004-02-24 22:58 8.9M
chr14.axt.gz 2004-02-24 22:58 30M
chr13_random.axt.gz 2004-02-24 22:58 3.4M
chr13.axt.gz 2004-02-24 22:58 49M
chr12_random.axt.gz 2004-02-24 22:58 3.7M
chr12.axt.gz 2004-02-24 22:58 41M
chr11_random.axt.gz 2004-02-24 22:57 3.1M
chr11.axt.gz 2004-02-24 22:57 41M
chr10_random.axt.gz 2004-02-24 22:57 2.8M
chr10.axt.gz 2004-02-24 22:57 39M
chr9_random.axt.gz 2004-02-24 22:58 4.9M
chr9.axt.gz 2004-02-24 22:58 65M
chr8_random.axt.gz 2004-02-24 22:58 5.1M
chr8.axt.gz 2004-02-24 22:58 66M
chr7_random.axt.gz 2004-02-24 22:58 4.7M
chr7.axt.gz 2004-02-24 22:58 73M
chr6_random.axt.gz 2004-02-24 22:58 8.0M
chr6.axt.gz 2004-02-24 22:58 74M
chr5_random.axt.gz 2004-02-24 22:58 6.2M
chr5.axt.gz 2004-02-24 22:58 86M
chr4_random.axt.gz 2004-02-24 22:58 5.8M
chr4.axt.gz 2004-02-24 22:58 90M
chr3_random.axt.gz 2004-02-24 22:58 5.7M
chr3.axt.gz 2004-02-24 22:58 95M
chr2_random.axt.gz 2004-02-24 22:58 6.4M
chr2.axt.gz 2004-02-24 22:58 100M
chr1_random.axt.gz 2004-02-24 22:58 9.8M
chr1.axt.gz 2004-02-24 22:57 82M