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 -
chrM.axt.gz 2004-02-24 22:58 820
md5sum.txt 2004-02-25 10:03 2.5K
chrY_random.axt.gz 2004-02-24 22:58 1.0M
chr22_random.axt.gz 2004-02-24 22:58 1.0M
chr23_random.axt.gz 2004-02-24 22:58 1.3M
chr15_random.axt.gz 2004-02-24 22:58 1.8M
chr21_random.axt.gz 2004-02-24 22:58 2.0M
chr20_random.axt.gz 2004-02-24 22:58 2.2M
chr10_random.axt.gz 2004-02-24 22:57 2.8M
chrY.axt.gz 2004-02-24 22:58 3.0M
chr11_random.axt.gz 2004-02-24 22:57 3.1M
chr13_random.axt.gz 2004-02-24 22:58 3.4M
chr18_random.axt.gz 2004-02-24 22:58 3.5M
chr12_random.axt.gz 2004-02-24 22:58 3.7M
chrX_random.axt.gz 2004-02-24 22:58 4.3M
chr17_random.axt.gz 2004-02-24 22:58 4.6M
chr7_random.axt.gz 2004-02-24 22:58 4.7M
chr9_random.axt.gz 2004-02-24 22:58 4.9M
chr8_random.axt.gz 2004-02-24 22:58 5.1M
chr16_random.axt.gz 2004-02-24 22:58 5.1M
chr3_random.axt.gz 2004-02-24 22:58 5.7M
chr4_random.axt.gz 2004-02-24 22:58 5.8M
chr5_random.axt.gz 2004-02-24 22:58 6.2M
chr2_random.axt.gz 2004-02-24 22:58 6.4M
chr6_random.axt.gz 2004-02-24 22:58 8.0M
chr14_random.axt.gz 2004-02-24 22:58 8.9M
chr1_random.axt.gz 2004-02-24 22:58 9.8M
chr19_random.axt.gz 2004-02-24 22:58 15M
chr23.axt.gz 2004-02-24 22:58 15M
chr22.axt.gz 2004-02-24 22:58 17M
chr20.axt.gz 2004-02-24 22:58 24M
chr19.axt.gz 2004-02-24 22:58 26M
chr21.axt.gz 2004-02-24 22:58 30M
chr14.axt.gz 2004-02-24 22:58 30M
chr15.axt.gz 2004-02-24 22:58 33M
chr18.axt.gz 2004-02-24 22:58 35M
chr17.axt.gz 2004-02-24 22:58 37M
chr16.axt.gz 2004-02-24 22:58 38M
chrUn_random.axt.gz 2004-02-24 22:58 39M
chr10.axt.gz 2004-02-24 22:57 39M
chr12.axt.gz 2004-02-24 22:58 41M
chr11.axt.gz 2004-02-24 22:57 41M
chrX.axt.gz 2004-02-24 22:58 47M
chr13.axt.gz 2004-02-24 22:58 49M
chr9.axt.gz 2004-02-24 22:58 65M
chr8.axt.gz 2004-02-24 22:58 66M
chr7.axt.gz 2004-02-24 22:58 73M
chr6.axt.gz 2004-02-24 22:58 74M
chr1.axt.gz 2004-02-24 22:57 82M
chr5.axt.gz 2004-02-24 22:58 86M
chr4.axt.gz 2004-02-24 22:58 90M
chr3.axt.gz 2004-02-24 22:58 95M
chr2.axt.gz 2004-02-24 22:58 100M