This directory contains the Jun. 2007 assembly of the starlet sea anemone genome
(nemVec1, US DOE JGI-PGF Nemve1), as well as repeat annotations and GenBank sequences.

This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the starlet sea anemone genome, see the project website:
http://genome.jgi-psf.org/Nemve1/Nemve1.download.html

Files included in this directory:

nemVec1.agp.gz - Description of how the assembly was generated from
    fragments.

nemVec1.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.

nemVec1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

nemVec1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)

nemVec1.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 - Starlet sea anemone ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

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.

nemVec1.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 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/nemVec1/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/nemVec1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nemVec1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nemVec1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nemVec1/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

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 these data
   (DOE Joint Genome Institute) is properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. *** PLEASE ADD PUBLICATION PLANS, IF ANY ***

4. Any redistribution of the data should carry this notice.