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 -
chr1.chain.gz 28-Sep-2004 17:07 66M
chr1_random.chain.gz 28-Sep-2004 17:07 5.1M
chr2.chain.gz 28-Sep-2004 17:07 49M
chr2_random.chain.gz 28-Sep-2004 17:07 116K
chr3.chain.gz 28-Sep-2004 17:07 41M
chr3_random.chain.gz 28-Sep-2004 17:07 4.1M
chr4.chain.gz 28-Sep-2004 17:07 34M
chr4_random.chain.gz 28-Sep-2004 17:07 6.4M
chr5.chain.gz 28-Sep-2004 17:07 38M
chr5_random.chain.gz 28-Sep-2004 17:07 1.8M
chr6.chain.gz 28-Sep-2004 17:07 29M
chr6_hla_hap1.chain.gz 28-Sep-2004 17:07 27K
chr6_hla_hap2.chain.gz 28-Sep-2004 17:07 31K
chr6_random.chain.gz 28-Sep-2004 17:07 484K
chr7.chain.gz 28-Sep-2004 17:07 144M
chr7_random.chain.gz 28-Sep-2004 17:07 307K
chr8.chain.gz 28-Sep-2004 17:07 30M
chr8_random.chain.gz 28-Sep-2004 17:07 57K
chr9.chain.gz 28-Sep-2004 17:07 60M
chr9_random.chain.gz 28-Sep-2004 17:07 448K
chr10.chain.gz 28-Sep-2004 17:07 35M
chr10_random.chain.gz 28-Sep-2004 17:07 7.9K
chr11.chain.gz 28-Sep-2004 17:07 37M
chr12.chain.gz 28-Sep-2004 17:07 23M
chr12_random.chain.gz 28-Sep-2004 17:07 199K
chr13.chain.gz 28-Sep-2004 17:07 15M
chr13_random.chain.gz 28-Sep-2004 17:07 589K
chr14.chain.gz 28-Sep-2004 17:07 32M
chr15.chain.gz 28-Sep-2004 17:07 14M
chr15_random.chain.gz 28-Sep-2004 17:07 321K
chr16.chain.gz 28-Sep-2004 17:07 30M
chr16_random.chain.gz 28-Sep-2004 17:07 10K
chr17.chain.gz 28-Sep-2004 17:07 25M
chr17_random.chain.gz 28-Sep-2004 17:07 2.8M
chr18.chain.gz 28-Sep-2004 17:07 16M
chr18_random.chain.gz 28-Sep-2004 17:07 8.5K
chr19.chain.gz 28-Sep-2004 17:07 384M
chr19_random.chain.gz 28-Sep-2004 17:07 778K
chr20.chain.gz 28-Sep-2004 17:07 16M
chr21.chain.gz 28-Sep-2004 17:07 7.8M
chr22.chain.gz 28-Sep-2004 17:07 25M
chr22_random.chain.gz 28-Sep-2004 17:07 1.0M
chrM.chain.gz 28-Sep-2004 17:07 33K
chrX.chain.gz 28-Sep-2004 17:07 36M
chrX_random.chain.gz 28-Sep-2004 17:07 679K
chrY.chain.gz 28-Sep-2004 17:07 41M
md5sum.txt 30-Jan-2005 08:43 2.3K