This directory contains the Oct. 2004 assembly of the Xenopus tropicalis
genome (xenTro1, Oct. 2004) from the DOE Joint Genome Institute (JGI).

Files included in this directory:

xenTro1.2bit - contains the complete X. tropicalis/xenTro1 genome sequence
    in the 2bit file format.  Repeats from RepeatMasker and Tandem Repeats
    Finder (with period of 12 or less) are shown in lower case; non-repeating
    sequence is shown in upper case.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

RmLib.zip - The RepeatMasker library file, xt3.lib1.fasta, 
    downloaded from JGI, 10/15/04.
    
est.fa.gz - X. tropicalis ESTs in GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

hardmask2.zip - The hard masked file.  The assembly sequence in one 
    file.  Repeats are masked by capital Ns; non-repeating sequence is 
    shown in upper case.  

md5sum.txt - MD5 checksum of these files to verify correct transmission.

mrna.fa.gz - X. tropicalis mRNA from GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

repeats.zip - RepeatMasker .out file for scaffolds. These were 
    created by RepeatMasker at the -s sensitive setting.

scaffolds.zip - The assembly sequence file that contains all
    scaffolds in one file, xenopus.041015.fasta, 
    downloaded from JGI, 10/15/04.

softmask2.zip - The soft Masked file.  The assembly sequence in 
    one file.  Repeats from RepeatMasker and Tandem Repeats Finder 
    (with period of 12 or less) are shown in lower case; non-repeating 
    sequence is shown in upper case.

trf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one 
    .bed file.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.


xenTro1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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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/bigZips. 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.