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