This directory contains alignments of the following assemblies:

  - target/reference: Mouse (mm8, Feb. 2006, NCBI Build 36)

  - query: Zebrafish (danRer4, Mar. 2006, Sanger Centre, Danio rerio Sequencing Project Zv6)

Files included in this directory:

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

  - mm8.danRer4.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - mm8.danRer4.net.gz: "net" file that describes rearrangements between 
    the species and the best Zebrafish match to any part of the
    Mouse genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - axtNet/*.mm8.danRer4.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Mouse 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 mm8 and danRer4 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 mm8 sequences larger
than 20,010,000 bases were split into chunks of 20,010,000 bases overlapping
by 10,000 bases for alignment.  A similar process was followed for danRer4,
with chunks of 300,000,000 overlapping by 0. These chunks were large enough 
to contain a single danRer4 chromsome in order for some dynamic masking to 
be effective (M parameter). Following alignment, the coordinates of the 
chunk alignments were corrected by the blastz-normalizeLav script written 
by Scott Schwartz of Penn State. Transposons that have been inserted since 
the Zebrafish/Mouse split were removed from the assemblies before alignment 
using the fasta-subseq and strip_rpts programs from Penn State.  The 
abbreviated genomes were aligned with blastz, and the transposons were then 
added back in (i.e. the alignment coordinates were adjusted) using the 
restore_rpts program from Penn State. There are no lineage-specific repeats 
defined for human and zebrafish so all repeats from each species were used 
as lineage-specific.

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:
    M=50
    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.

----------------------------------------------------------------
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/mm8/vsDanRer4/. To download multiple files, use the "mget"
command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all files in the current directory)

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.txt24-May-2006 15:22 4.6K 
[DIR]axtNet/10-May-2011 16:54 -  
[TXT]md5sum.txt23-May-2006 22:01 2.3K 
[   ]mm8.danRer4.all.chain.gz23-May-2006 14:16 21M 
[   ]mm8.danRer4.net.gz23-May-2006 22:00 9.9M 

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