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 - md5sum.txt 2005-01-30 08:43 2.3K chr10_random.chain.gz 2004-09-28 17:07 7.9K chr18_random.chain.gz 2004-09-28 17:07 8.5K chr16_random.chain.gz 2004-09-28 17:07 10K chr6_hla_hap1.chain.gz 2004-09-28 17:07 27K chr6_hla_hap2.chain.gz 2004-09-28 17:07 31K chrM.chain.gz 2004-09-28 17:07 33K chr8_random.chain.gz 2004-09-28 17:07 57K chr2_random.chain.gz 2004-09-28 17:07 116K chr12_random.chain.gz 2004-09-28 17:07 199K chr7_random.chain.gz 2004-09-28 17:07 307K chr15_random.chain.gz 2004-09-28 17:07 321K chr9_random.chain.gz 2004-09-28 17:07 448K chr6_random.chain.gz 2004-09-28 17:07 484K chr13_random.chain.gz 2004-09-28 17:07 589K chrX_random.chain.gz 2004-09-28 17:07 679K chr19_random.chain.gz 2004-09-28 17:07 778K chr22_random.chain.gz 2004-09-28 17:07 1.0M chr5_random.chain.gz 2004-09-28 17:07 1.8M chr17_random.chain.gz 2004-09-28 17:07 2.8M chr3_random.chain.gz 2004-09-28 17:07 4.1M chr1_random.chain.gz 2004-09-28 17:07 5.1M chr4_random.chain.gz 2004-09-28 17:07 6.4M chr21.chain.gz 2004-09-28 17:07 7.8M chr15.chain.gz 2004-09-28 17:07 14M chr13.chain.gz 2004-09-28 17:07 15M chr18.chain.gz 2004-09-28 17:07 16M chr20.chain.gz 2004-09-28 17:07 16M chr12.chain.gz 2004-09-28 17:07 23M chr22.chain.gz 2004-09-28 17:07 25M chr17.chain.gz 2004-09-28 17:07 25M chr6.chain.gz 2004-09-28 17:07 29M chr16.chain.gz 2004-09-28 17:07 30M chr8.chain.gz 2004-09-28 17:07 30M chr14.chain.gz 2004-09-28 17:07 32M chr4.chain.gz 2004-09-28 17:07 34M chr10.chain.gz 2004-09-28 17:07 35M chrX.chain.gz 2004-09-28 17:07 36M chr11.chain.gz 2004-09-28 17:07 37M chr5.chain.gz 2004-09-28 17:07 38M chrY.chain.gz 2004-09-28 17:07 41M chr3.chain.gz 2004-09-28 17:07 41M chr2.chain.gz 2004-09-28 17:07 49M chr9.chain.gz 2004-09-28 17:07 60M chr1.chain.gz 2004-09-28 17:07 66M chr7.chain.gz 2004-09-28 17:07 144M chr19.chain.gz 2004-09-28 17:07 384M