This directory contains alignments of the human assembly (hg17, May 2004)
to itself.
The chr*.chain.gz files are the chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
The md5sum.txt file indicates the md5 check sum of these chr*.chain.gz
files to verify a correct copy.
The alignments were produced by the blastz alignment program, which
is available from Webb Miller's lab at Penn State University
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:
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 is 2000.
Each chromosome was divided into 10,000,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt.
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If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/hg17/vsSelf/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the tables in this directory are freely available for public use.
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References
Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic
sequence alignments. Pac Symp Biocomput 2002;115-26.
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489
Sep 30 2003.
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1):103-7 (2003).
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Name Last modified Size Description
Parent Directory -
chr19.chain.gz 2004-09-28 17:07 384M
chr7.chain.gz 2004-09-28 17:07 144M
chr1.chain.gz 2004-09-28 17:07 66M
chr9.chain.gz 2004-09-28 17:07 60M
chr2.chain.gz 2004-09-28 17:07 49M
chr3.chain.gz 2004-09-28 17:07 41M
chrY.chain.gz 2004-09-28 17:07 41M
chr5.chain.gz 2004-09-28 17:07 38M
chr11.chain.gz 2004-09-28 17:07 37M
chrX.chain.gz 2004-09-28 17:07 36M
chr10.chain.gz 2004-09-28 17:07 35M
chr4.chain.gz 2004-09-28 17:07 34M
chr14.chain.gz 2004-09-28 17:07 32M
chr8.chain.gz 2004-09-28 17:07 30M
chr16.chain.gz 2004-09-28 17:07 30M
chr6.chain.gz 2004-09-28 17:07 29M
chr17.chain.gz 2004-09-28 17:07 25M
chr22.chain.gz 2004-09-28 17:07 25M
chr12.chain.gz 2004-09-28 17:07 23M
chr20.chain.gz 2004-09-28 17:07 16M
chr18.chain.gz 2004-09-28 17:07 16M
chr13.chain.gz 2004-09-28 17:07 15M
chr15.chain.gz 2004-09-28 17:07 14M
chr21.chain.gz 2004-09-28 17:07 7.8M
chr4_random.chain.gz 2004-09-28 17:07 6.4M
chr1_random.chain.gz 2004-09-28 17:07 5.1M
chr3_random.chain.gz 2004-09-28 17:07 4.1M
chr17_random.chain.gz 2004-09-28 17:07 2.8M
chr5_random.chain.gz 2004-09-28 17:07 1.8M
chr22_random.chain.gz 2004-09-28 17:07 1.0M
chr19_random.chain.gz 2004-09-28 17:07 778K
chrX_random.chain.gz 2004-09-28 17:07 679K
chr13_random.chain.gz 2004-09-28 17:07 589K
chr6_random.chain.gz 2004-09-28 17:07 484K
chr9_random.chain.gz 2004-09-28 17:07 448K
chr15_random.chain.gz 2004-09-28 17:07 321K
chr7_random.chain.gz 2004-09-28 17:07 307K
chr12_random.chain.gz 2004-09-28 17:07 199K
chr2_random.chain.gz 2004-09-28 17:07 116K
chr8_random.chain.gz 2004-09-28 17:07 57K
chrM.chain.gz 2004-09-28 17:07 33K
chr6_hla_hap2.chain.gz 2004-09-28 17:07 31K
chr6_hla_hap1.chain.gz 2004-09-28 17:07 27K
chr16_random.chain.gz 2004-09-28 17:07 10K
chr18_random.chain.gz 2004-09-28 17:07 8.5K
chr10_random.chain.gz 2004-09-28 17:07 7.9K
md5sum.txt 2005-01-30 08:43 2.3K