This directory contains alignments of the Tetraodon assembly 
(tetNig1, Feb. 2004) to the mouse assembly (mm5, May 2004).

Files included in this directory:

  - axtChrom 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. 

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

  - tetNig1.net.zip: "net" file that describes rearrangements between the 
    species and the best Tetraodon match to any part of the mouse 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 files in the axtChrom directory are in "axt" format. For a 
description, see http://genome.ucsc.edu/goldenPath/help/axt.html.

The axt 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 axtNet alignments were processed 
with chainNet, netSyntenic, and netClass written by Jim Kent at UCSC.

The blastz scoring matrix used for this alignment was HoxD55.q:

          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 6000 for the first 
pass, and 2000 for the second pass, which restricts the search space 
to just 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. Low scores 
can occur using the scoring matrix above and with repeats abridged so 
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

------------------------------------------------------------------
If you plan to download a large file or multiple files from this 
directory, we recommend that 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/mm5/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 usable for any 
purpose.  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.