This directory contains the Oct. 2004 preliminary assembly of the
Monodelphis domestica (South American, Short-tailed Opossum)
genome (monDom1, Oct. 2004) from the Broad Institute.

Files included in this directory:

hardMask.fa.gz -  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 - Checksums for the .gz files in this directory.
    Excluding mrna.fa.gz and xenoMrna.fa.gz since they change weekly.

mrna.fa.gz - GenBank mRNA sequences for Monodelphis domestica.
    This sequence data is updated once a week via automatic GenBank
    updates.

novel.RM.lib.fa.gz - additional Repeat Masker library
    representing novel sequences in addition to the standard
    mammal library repeats.  Created by Damian Keefe of Ensembl
    for the ENCODE project.  See also:
    ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/repeat_libraries/README
    http://www.nisc.nih.gov/open_page.html?/projects/encode/index.cgi

rmsk.sql - SQL structure for database table rmsk  (see rmsk.txt.gz)

rmsk.txt.gz - text dump of data base table rmsk - see also the SQL
    structure for this data base table in the file rmsk.sql
    This is the result from the Repeat Masker operation on the
    assembly.  The -s sensitive setting was used with Repeat Masker
    and library version: RepBase Update 9.04, RM database version 20040702

softMask.fa.gz - 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.bed.gz - 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 - All GenBank mRNA sequences except Monodelphis domestica 
    mRNA.  This sequence data is updated once a week via automatic GenBank
    updates.



monDom1.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/monDom1/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 opossum sequence are made freely available
before scientific publication by the Broad Institute, 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 
   (The Broad Institute) is properly acknowledged. 
3. The centers producing the data reserve the right to publish the 
   initial large-scale analyses of the data set, including large-scale 
   identification of regions of evolutionary conservation and large-scale 
   genomic assembly.  Large-scale refers to regions with size on the order 
   of a chromosome (that is, 30 Mb or more). 
4. Any redistribution of the data should carry this notice.