This directory contains alignments of the human assembly 
(hg17, Jul. 2003) to the chicken assembly (galGal2, 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 chicken 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 axtChrom 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  -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 10,000 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.

Each chromosome was divided into 10,010,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. 

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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/galGal2/vsHg16/. To download 
multiple files, use the "mget" command:

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

The chicken sequence is made freely available before scientific 
publication 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 providers of these data are 
   properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
   for credit information.
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.