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

Files included in this directory:

  - axtChrom directory: contains the axt alignments generated by blastz,
    in one file per chromosome. Blastz output was converted to lav format, 
    which was then converted to axt format. 

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

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

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

The alignments in the axtNet directory 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

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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/tetNig1/vsHg17/. To download multiple files, 
use the "mget" command:

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

All the tables in this directory are freely available for public use. 

The Tetraodon sequence has been freely provided by Genoscope before 
publication for use in the UCSC Genome Browser 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, provided that the Genoscope is properly acknowledged.
3. Genoscope reserves the right to publish the initial large-scale analyses 
   of the dataset, 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 Tetraodon chromosome (that 
   is, 5 Mb or more).
4. Any redistribution of the data should carry this notice.