This file is from:

   http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsSelf/README.txt

This directory contains alignments of Human (hg38, Dec. 2013, GRC Build GRCh38)
to itself, primary chromosomes only 1-22,X,Y,M

Files included in this directory:

  - md5sum.txt: md5sum checksums for the files in this directory

  - hg38.hg38.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

The hg38 assembly was aligned to itself by the lastz (v1.03.52) alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any hg38 sequences larger
than 20,000,000 bases were split into chunks of 20,010,000 bases overlapping
by 10,000 bases for alignment.  The query sequence, hg38, was split
into chunks of 20,000,000 overlapping by 0.  Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State. 

The lastz scoring matrix (Q parameter) used was the default lastz matrix:

           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 O=400, a gap extension penalty of E=30,
--x_drop X=910, --y_drop Y=9400, --hsp_threshold K=3000,
--gapped_threshold L=3000 --inner H=2000,
T=1 (--seed=12of19 1110100110010101111 --transition), --step Z=1

The .axt format lastz output was translated to the .psl format with
axtToPsl | pslDropOverlap to remove alignments of sequences to themselves,
then chained by the axtChain program.

Chain minimum score: 10000, and linearGap matrix of (medium):
tableSize   11
smallSize  111
position  1   2   3   11  111 2111  12111 32111  72111 152111  252111
qGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
tGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
bothGap 750 825 850 1000 1300 3300  23300 58300 118300 218300  318300

All programs run after lastz were written by Jim Kent at UCSC.

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg38/vsSelf

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

All files in this directory are freely available for public use.

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References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic
sequence alignments.  Pac Symp Biocomput 2002, 115-26 (2002).

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
(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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