This directory contains alignments of the following assemblies:

  - target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1)

  - query: Zebrafish (danRer3, May 2005, Sanger Centre, Danio rerio Sequencing 
    Project Zv5)

Files included in this directory:

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

  - hg18.danRer3.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - hg18.danRer3.net.gz: "net" file that describes rearrangements between 
    the species and the best Zebrafish match to any part of the
    Human genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.hg18.danRer3.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 hg18 and danRer3 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any hg18 sequences larger
than 10,010,000 bases were split into chunks of 10,010,000 bases overlapping
by 10,000 bases for alignment.  A similar process was followed for danRer3,
with 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. 

Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random 
chromosomes are comprised of unordered scaffolds separated by 500 <em>N</em>s
and 1000 <em>N</em>s respectively, the blastz alignments and subsequent 
chaining were first performed on the scaffolds, and the coordinates were then 
lifted up to the chromosome level. This avoided false alignments across the 
<em>N</em>s. Random unordered chromosomes from human were treated in a 
similar manner so that alignments were performed using the contigs whcih are 
separated by 50000 Ns. For alignments involving zebrafish chrNA and chrUn 
scaffolds,  lineage-specific repeats were not used, but the M parameter was 
set to 50 in order to utilize the Blastz dynamic masking functionality. Each 
chunk of human sequence was aligned with all of the zebrafish sequence in 
order for dynamic masking to occur. 

The blastz scoring matrix (Q parameter) used was:

             A    C    G    T
      A     91  -90  -25 -100
      C    -90  100 -100  -25
      G    -25 -100  100  -90
      T   -100  -25  -90  91

with a gap open penalty of O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=2200 for the first pass
and L=6000 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 blastz
parameters specifically set for this species pair:
    Y=3400

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

Chain minimum score: 5000, and linearGap matrix of (loose):
tablesize   11
smallSize   111   
position  1   2   3   11  111 2111  12111 32111 72111 152111  252111
qGap    325 360 400  450  600 1100   3600  7600 15600  31600   56600
tGap    325 360 400  450  600 1100   3600  7600 15600  31600   56600
bothGap 625 660 700  750  900 1400   4000  8000 16000  32000   57000

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz 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/hg18/vsDanRer3

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.txt02-Jul-2007 13:10 5.0K 
[DIR]axtNet/25-Sep-2008 09:32 -  
[   ]hg18.danRer3.all.chain.gz23-Dec-2005 11:18 24M 
[   ]hg18.danRer3.net.gz23-Dec-2005 12:02 12M 
[TXT]md5sum.txt23-Dec-2005 12:03 3.6K 

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