This directory contains alignments of the Tetraodon assembly 
(tetNig1, Feb. 2004) to the human assembly (hg17, May 2004).

Files included in this directory:

  - axtNet directory: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in 
    by next-best chains where possible. 

  - axtTight directory: contains a highly conserved subset of the best 
    alignments for any part of the human genome. 

  - tetNig1.chain.gz: chained blastz alignments. The chain format is 
    described in http://genome.ucsc.edu/goldenPath/help/chain.html.

  - tetNig1.net.gz: "net" file that describes rearrangements between the 
    species and the best Tetraodon match to any part of the human genome.  
    The net format is described in 
    http://genome.ucsc.edu/goldenPath/help/net.html.

The alignments in the axtNet and axtTight directories are in "axt" format. 
For a description, see http://genome.ucsc.edu/goldenPath/help/axt.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 -114  -31 -123
      C -114  100 -125  -31
      G  -31 -125  100 -114
      T -123  -31 -114   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 3000 for the first pass  
and 2000 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.

Each chromosome was divided into 10,000,000 base chunks for the blastz 
alignments and all repeats for each organism were used as lineage-specific 
repeats. Repeats were detected with Arian Smit's RepeatMasker program. 
The .lav format blastz output, which does not include the sequence, was 
converted to .axt with lavToAxt.

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


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

----------------------------------------------------------------
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/hg17/vsTetNig1/. To download multiple 
files, use the "mget" command:

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

All the 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.

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).

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