This directory contains alignments of the human assembly (hg16, Jul. 2003)
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/hg16/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.

--------------------------------------------------------------------
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).
      Name                    Last modified      Size  Description
Parent Directory - chr1.chain.gz 2003-09-08 12:52 59M chr1_random.chain.gz 2003-09-08 12:52 5.5M chr2.chain.gz 2003-09-08 12:52 45M chr2_random.chain.gz 2003-09-08 12:52 86K chr3.chain.gz 2003-09-08 12:52 40M chr3_random.chain.gz 2003-09-08 12:52 33K chr4.chain.gz 2003-09-08 12:52 35M chr4_random.chain.gz 2003-09-08 12:52 27K chr5.chain.gz 2003-09-08 12:52 39M chr5_random.chain.gz 2003-09-08 12:52 1.9M chr6.chain.gz 2003-09-08 12:52 29M chr6_random.chain.gz 2003-09-08 12:52 340K chr7.chain.gz 2003-09-08 12:52 143M chr7_random.chain.gz 2003-09-08 12:52 157K chr8.chain.gz 2003-09-08 12:52 30M chr8_random.chain.gz 2003-09-08 12:52 78K chr9.chain.gz 2003-09-08 12:52 55M chr9_random.chain.gz 2003-09-08 12:52 610K chr10.chain.gz 2003-09-08 12:52 36M chr10_random.chain.gz 2003-09-08 12:52 136K chr11.chain.gz 2003-09-08 12:52 39M chr12.chain.gz 2003-09-08 12:52 23M chr13.chain.gz 2003-09-08 12:52 14M chr13_random.chain.gz 2003-09-08 12:52 494K chr14.chain.gz 2003-09-08 12:52 12M chr15.chain.gz 2003-09-08 12:52 14M chr15_random.chain.gz 2003-09-08 12:52 333K chr16.chain.gz 2003-09-08 12:52 32M chr17.chain.gz 2003-09-08 12:52 25M chr17_random.chain.gz 2003-09-08 12:52 2.3M chr18.chain.gz 2003-09-08 12:52 16M chr18_random.chain.gz 2003-09-08 12:52 112 chr19.chain.gz 2003-09-08 12:52 194M chr19_random.chain.gz 2003-09-08 12:52 134 chr20.chain.gz 2003-09-08 12:52 15M chr21.chain.gz 2003-09-08 12:52 7.8M chr22.chain.gz 2003-09-08 12:52 20M chrM.chain.gz 2003-09-08 12:52 36K chrUn_random.chain.gz 2003-09-08 12:52 8.7M chrX.chain.gz 2003-09-08 12:52 34M chrX_random.chain.gz 2003-09-08 12:52 318K chrY.chain.gz 2003-09-08 12:52 41M md5sum.txt 2005-01-27 11:01 2.1K