This directory contains the Monodelphis domestica genome 
(UCSC monDom5, October 2006) from The Broad Institute.

Files included in this directory:

Monodelphis5.0.agp.gz - Description of how the assembly was generated from
     fragments.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    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.  

chromFaMasked.tar.gz - The assembly sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

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

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

monDom5.2bit - contains the complete monDom5 Opossum Genome
    in the 2bit format.  A utility program, twoBitToFa (available
    from our source tree), can be used to extract .fa file(s) from
    this file.  See also:
	http://genome.ucsc.edu/admin/cvs.html - CVS access to the source tree
	http://genome.ucsc.edu/admin/jk-install.html - building the utilities

monDom5.quals.fa.gz - quality scores in fasta file format

est.fa.gz - Mouse 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 - Opossum 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 for RefSeq genes with annotated 5' UTRs.
    This file is updated weekly so it could be slightly out
    of sync with the RefSeq data which is updated daily for most
    assemblies.

upstream2000.zip - Same as upstream1000, but 2000 bases.

upstream5000.zip - Same as upstream1000, but 5000 bases.

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.


monDom5.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

monDom5.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

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If you plan to download a large file or multiple files from this directory, 
we recommend you use rsync, wget, or ftp rather than downloading the
files via our website. To do so, anonymous ftp to hgdownload.cse.ucsc.edu,
go to the directory goldenPath/monDom5/bigZips/.

To download multiple files via ftp, use the "mget" command:
mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

The rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP \
     rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping \
	'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/*'
With wget, a single file:
    wget --timestamping \
    'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/chromFa.tar.gz' \
	-O chromFa.tar.gz

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

All files in this directory are freely usable for any purpose. 

This file last updated: 2009-06-10 - 10 June 2009