This directory contains alignments of the Fugu assembly 
(fr1, Aug. 2002) to the Tetraodon assembly (tetNig1, Feb. 2004)
in "axt" format. For a description, 

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
( 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 8000 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.

Each chromosome was divided into 10,010,000 base chunks for the blastz
alignments. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. There are no 
lineage-specific repeats available for these two fish; therefore, none 
were used in the blastz alignments.

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, then go to 
the directory goldenPath/tetNig1/vsFr1/. 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 

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.
      Name                       Last modified      Size  Description
Parent Directory - chr1.axt 2004-08-31 21:37 56M chr1_random.axt 2004-08-31 21:41 11M chr2.axt 2004-08-31 21:41 50M chr2_random.axt 2004-08-31 21:41 5.4M chr3.axt 2004-08-31 21:41 38M chr3_random.axt 2004-08-31 21:41 1.2M chr4.axt 2004-08-31 21:41 14M chr5.axt 2004-08-31 21:41 26M chr6.axt 2004-08-31 21:41 13M chr7.axt 2004-08-31 21:41 29M chr8.axt 2004-08-31 21:41 22M chr9.axt 2004-08-31 21:41 26M chr10.axt 2004-08-31 21:37 31M chr11.axt 2004-08-31 21:37 28M chr12.axt 2004-08-31 21:37 29M chr13.axt 2004-08-31 21:37 28M chr14.axt 2004-08-31 21:37 22M chr15.axt 2004-08-31 21:37 18M chr15_random.axt 2004-08-31 21:37 7.5M chr16.axt 2004-08-31 21:37 24M chr17.axt 2004-08-31 21:37 25M chr18.axt 2004-08-31 21:41 29M chr19.axt 2004-08-31 21:41 12M chr20.axt 2004-08-31 21:41 5.5M chr21.axt 2004-08-31 21:41 15M chr21_random.axt 2004-08-31 21:41 7.0M chrUn_random.axt 2004-08-31 21:42 577M