This directory contains the April 2005 Spur_0.5 release of the 
S. purpuratus genome (strPur1) obtained from the Baylor College of 
Medicine Human Genome Sequencing Center.

Files included in this directory:

strPur1.2bit - contains the complete S. purpuratus/strPur1 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

allAgp.tar.gz - Description of how the assembly was generated from
     fragments. 

allFa.tar.gz- Sequences downloaded from Baylor 19 April 2005.

allFaMasked.tar.gz - The assembly sequence with repeats 
    masked by capital Ns; non-repeating sequence is shown in upper case.  

allOut.tar.gz - RepeatMasker .out file for chromosomes. These were created 
    by RepeatMasker at the -s sensitive setting.

allTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one 
    .bed file per chromosomes.  

md5sum.txt - Checksum file.

mrna.fa.gz - S. purpuratus 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.

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.

strPur1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

-----------------------------------------------------------------
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/strPur1/bigZips. To download multiple files, 
use the "mget" command:

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

These data are made 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. 
Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to 
the genome sequence. 
3. BCM HGSC plans to publish the assembly and genomic annotation of the dataset,
including large-scale identification of regions of evolutionary conservation. 
4. This is in accordance with, and with the understandings in the Fort 
Lauderdale meeting discussing Community Resource Projects and the resulting 
NHGRI policy statement. 
5. Any redistribution of the data should carry this notice.