This directory contains alignments of the zebrafish assembly 
(danRer2, June 2004) to the opossum assembly (monDom1, October 2004).

Files included in this directory:

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

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

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix 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 400 and a gap extension penalty of 30.  The 
minimum score for an alignment to be kept was 5,000 for the first pass  
and 2200 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.  Extra blastz
parameters:
  H=2000 interpolate between alignments at threshold K = 2000.
  K=2200 threshold for MSPs.
  L=10000 threshold for gapped alignments.
  Y=3400  X-drop parameter for gapped extension.

Each chromosome or scaffold was divided into 10,000,000 base chunks for the
blastz alignments.  No lineage specific repeats were used in these alignments.
The .lav format blastz output, which does not include the sequence, was
converted to .axt with lavToAxt. Low scores can occur using the scoring
matrix above and with repeats abridged; therefore, alignments were rescored
using PSU's restore_rpts program and the default scoring matrix:

         A    C    G    T
    A   91 -114  -31 -123
    C -114  100 -125  -31
    G  -31 -125  100 -114
    T -123  -31 -114   91

For chaining, the axtChain linearGap option was used to specify gap 
penalties:

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

Chains produced by axtChain were also filtered with a minimum score of 5000 
and then chainAntiRepeat was applied to remove chains that are primarily the
result of repeats and degenerate DNA.

----------------------------------------------------------------
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/monDom1/vsDanRer2/. To download multiple 
files, use the "mget" command:

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

Preliminary drafts of the opossum sequence are made freely available
before scientific publication by the Broad Institute, with the following 
understanding:

1. The data may be freely downloaded, used in analyses, and repackaged 
   in databases. 
2. Users are free to use the data in scientific papers analyzing 
   particular genes and regions if the provider of this data 
   (The Broad Institute) is properly acknowledged. 
3. The centers producing the data reserve the right to publish the 
   initial large-scale analyses of the data set, including large-scale 
   identification of regions of evolutionary conservation and large-scale 
   genomic assembly.  Large-scale refers to regions with size on the order 
   of a chromosome (that is, 30 Mb or more). 
4. Any redistribution of the data should carry this notice. 

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

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic 
sequence alignments.  Pac Symp Biocomput 2002;115-26.

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 
Sep 30 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.txt18-Feb-2005 11:52 4.4K 

Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80