This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (JGI 4.2/xenTro3) assembly of the
Xenopus (Silurana) tropicalis (western clawed frog) genome
(xenTro3, US DOE Joint Genome Institute (JGI-PGF)
(GCA_000004195.1)) from the X. tropicalis Genome Consortium.
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the X. tropicalis genome, please note the
NCBI WGS Traces information:
	http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01
and the project website:
	http://genome.jgi-psf.org/Xentr4/Xentr4.home.html

Files included in this directory:

xenTro3.2bit - contains the complete X. tropicalis/xenTro3 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

xenTro3.agp.gz - Description of how the assembly was generated from
    fragments.

xenTro3.fa.gz - "Soft-masked" 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.

xenTro3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

xenTro3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  RepeatMasker version: June 30 2010 (open-3-2-9)
    library version RELEASE 20090604

xenTro3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

est.fa.gz - X. tropicalis ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

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

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    This sequence data is updated once a week via automatic GenBank
    updates.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts of RefSeq genes with annotated 5' UTRs.
    This file is updated weekly so it might be slightly out of sync with
    the RefSeq data which is updated daily for most assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.


xenTro3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

xenTro3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
xenTro3.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
xenTro3.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:  http://genome.ucsc.edu/goldenPath/help/wiggle.html
    and  http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

xenTro3.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

------------------------------------------------------------------
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/xenTro3/bigZips. To download multiple files, use
the "mget" command:

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

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

==========================================================================
Data use policy from:
    http://genome.jgi-psf.org/Xentr4/Xentr4.download.html

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. 
==========================================================================
      Name                          Last modified      Size  Description
Parent Directory - est.fa.gz 2019-10-17 22:50 306M est.fa.gz.md5 2019-10-17 22:50 44 genes/ 2020-02-05 13:47 - md5sum.txt 2019-01-17 15:59 638 mrna.fa.gz 2019-10-17 22:46 14M mrna.fa.gz.md5 2019-10-17 22:46 45 refMrna.fa.gz 2019-10-17 22:50 6.7M refMrna.fa.gz.md5 2019-10-17 22:50 48 upstream1000.fa.gz 2019-10-17 22:51 1.9M upstream1000.fa.gz.md5 2019-10-17 22:51 53 upstream2000.fa.gz 2019-10-17 22:51 3.6M upstream2000.fa.gz.md5 2019-10-17 22:51 53 upstream5000.fa.gz 2019-10-17 22:51 8.7M upstream5000.fa.gz.md5 2019-10-17 22:51 53 xenTro3.2bit 2011-09-09 10:23 373M xenTro3.agp.gz 2011-09-16 10:09 4.3M xenTro3.chrom.sizes 2011-09-08 10:05 275K xenTro3.chromAlias.txt 2020-09-29 10:49 382K xenTro3.fa.gz 2011-09-16 10:16 415M xenTro3.fa.masked.gz 2011-09-16 10:23 315M xenTro3.fa.out.gz 2011-09-16 10:10 50M xenTro3.gc5Base.wib 2019-01-17 14:53 267M xenTro3.gc5Base.wig.gz 2019-01-17 14:53 6.1M xenTro3.gc5Base.wigVarStep.gz 2011-09-08 10:11 674M xenTro3.trf.bed.gz 2011-09-16 10:10 1.8M