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.
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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/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.
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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).
Name Last modified Size Description
Parent Directory -
hg19.hg19.all.chain.gz 2009-03-19 13:09 34M
hg19.hg19.net.gz 2011-04-12 16:07 6.1M
md5sum.txt 2011-04-12 16:08 108
axtNet/ 2011-04-15 14:48 -