This directory contains zipped multiple alignments of the X. tropicalis
genome (xenTro1, Oct. 2004) to the following assemblies:

 - Chicken (galGal2, Feb. 2004)
 - Human (hg17, May 2004)
 - Mouse (mm5, May 2004)
 - Zebrafish (danRer1, Nov. 2003)

Files included in this directory:

  - danRer1.maf.gz: pairwise alignment of zebrafish (danRer1) and 
    X. tropicalis

  - galGal2.maf.gz: pairwise alignment of chicken (galGal2) and 
    X. tropicalis

  - hg17.maf.gz: pairwise alignment of human (hg17) and X. tropicalis

  - md5sum.txt: checksums of files in this directory

  - mm5.maf.gz: pairwise alignment of mouse (mm5) and X. tropicalis

  - multiz5way.maf.gz: multiple alignments in MAF format 

For a description of the multiple alignment format (MAF), see 
http://genome.ucsc.edu/goldenPath/help/maf.html.

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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/xenTro1/multiz5way. To download 
multiple files, use the "mget" command:

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

Preliminary drafts of the X. tropicalis sequence are made freely available
before scientific publication by the JGI and the X. tropicalis Genome 
Consortium, 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 provider of this data 
   (DOE Joint Genome Institute) is properly acknowledged. 
3. Additional shotgun sequencing is ongoing, and future assembly 
   releases will be made in a timely fashion. We expect to publish an 
   initial analysis of a high quality draft X. tropicalis genome sequence 
   in 2005 (with submission targeted for the spring of 2005) which will 
   include descriptions of the large scale organization of the frog 
   genome as well as genome-scale comparisons of the frog sequence and 
   gene set with those of other animals. Others who would like to 
   coordinate other genome-wide analysis with this work should contact
   Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated 
   approach to describing this community resource. 
4. Any redistribution of the data should carry this notice. 

For data use restrictions regarding the chicken and zebrafish genome
assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
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