This directory contains the Monodelphis domestica genome 
(UCSC monDom4, January 2006) from The Broad Institute.

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.
    Each chromosome is in a separate file in a gzip Fasta format. 
    Repeats -- which are shown in lower case -- are annotated by 
    RepeatMasker run at the sensitive setting and Tandem Repeats Finder
    (repeats of period 12 or less).  Repeat Masker database version: 20060120

md5sum.txt - MD5 checksum of these files to verify correct transmission

The main assembly is contained in the chrN.fa.gz files, where N is the name 
of the chromosome.  The chrUn.fa.gz file contains clones that are not 
yet finished or cannot be placed with certainty at a specific place on 
any chromosome.

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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, then 
go to the directory goldenPath/monDom4/chromosomes. To download multiple 
files, 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/monDom4/chromosomes/ .
For a single file, e.g. chrX.fa.gz
    rsync -avzP \
     rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom4/chromosomes/chrX.fa.gz .

Or with wget, all files:
    wget --timestamping \
	'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/chromosomes/*'
With wget, a single file:
    wget --timestamping \
    'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/chromosomes/chrX.fa.gz' \
	-O chrX.fa.gz

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

All the files in this directory are freely available for public use.

This file last updated: 2006-05-15 - 15 May 2006