This directory contains alignments of the following assemblies:

  - target/reference: Mouse (mm9, Jul. 2007, NCBI Build 37)

  - query: Rat (rn4, Nov. 2004, Baylor HGSC v. 3.4)

Files included in this directory:

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

  - mm9.rn4.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - mm9.rn4.net.gz: "net" file that describes rearrangements between 
    the species and the best Rat match to any part of the
    Mouse genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - mm9.rn4.syn.net.gz: "syntenic net" file.  This is the net
    filtered to remove non-syntenic alignments

  - axtNet/*.mm9.rn4.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 mm9 and rn4 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 mm9 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 rn4,
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. 

The blastz scoring matrix (Q parameter) used was:

            A    C    G    T
      A     56 -109  -45 -137
      C   -109  100 -103  -45
      G    -45 -103  100 -109
      T   -137  -45 -109   56

with a gap open penalty of O=600 and a gap extension penalty of E=55.
The minimum score for an alignment to be kept was K=4500 for the first pass
and L=2200 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:
    E=55
    O=600
    T=2
    Y=15000

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 (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

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/mm9/vsRn4/. 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.txt07-Nov-2007 14:31 4.0K 
[DIR]axtNet/10-May-2011 16:55 -  
[TXT]md5sum.txt07-Nov-2007 13:58 2.4K 
[   ]mm9.rn4.all.chain.gz31-Aug-2007 16:17 189M 
[   ]mm9.rn4.net.gz04-Sep-2007 12:49 130M 
[   ]mm9.rn4.syn.net.gz07-Nov-2007 12:04 123M 

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