This directory contains alignments of Human (hg19, Feb. 2006, NCBI Build GRCh37) 
to itself.

Files included in this directory:

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

  - hg19.hg19.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - hg19.hg19.net.gz: "net" file that describes duplications/
    rearrangements and the best-in-genome match to any other part of
    the genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.hg19.hg19.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Human genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in http://genome.ucsc.edu/goldenPath/help/axt.html .

The hg19 assembly was aligned to itself by the lastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any hg19 sequences larger
than 10,010,000 bases were split into chunks of 10,010,000 bases overlapping
by 10,000 bases for alignment.  The query sequence, hg19, was split
into chunks of 10,000,000 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 human-chimp matrix:

           A    C    G    T
      A   90 -330 -236 -356
      C -330  100 -318 -236
      G -236 -318  100 -330
      T -356 -236 -330   90

with a gap open penalty of O=600 and a gap extension penalty of E=150.
The minimum score for an alignment to be kept was K=10000 for the first pass
and L=10000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.  The minimum
score for alignments to be interpolated between was H=2000.  Other lastz
parameters specifically set for this self alignment:
    M=254, T=2, Y=15000

The .lav format lastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.

Chain minimum score: 2000, 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.

----------------------------------------------------------------
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/hg19/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.

--------------------------------------------------------------------
References

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).


[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt15-Apr-2011 14:49 3.9K 
[DIR]axtNet/15-Apr-2011 14:48 -  
[   ]hg19.hg19.all.chain.gz19-Mar-2009 13:09 34M 
[   ]hg19.hg19.net.gz12-Apr-2011 16:07 6.1M 
[TXT]md5sum.txt12-Apr-2011 16:08 108  

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