This directory contains the Build 34 assembly of the mouse genome 
(UCSC mm6, March 2005) from the Mouse Genome Sequencing Consortium. This 
assembly was produced at NCBI.  

Files included in this directory:

chromAgp.tar.gz - Description of how the assembly was generated from
     fragments, unpacking to one file per chromosome.  

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.  RepeatMasker January 12 2005 version with RepBase
    libraries: RepBase Update 9.11, RM database version 20050112

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.  

est.fa.gz - Mouse ESTs from GenBank, updated once a week via automatic 
    GenBank updates.

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

mrna.fa.gz - Mouse mRNA from GenBank, updated once a week via automatic 
    GenBank updates.

refMrna.fa.gz - RefSeq mRNA from the same species as the genome, updated 
    once a week via automatic GenBank updates.

upstream1000.zip - Sequences 1000 bases upstream of annotated
    transcription start of RefSeq genes.  This includes only the
    cases where the transcription start is annotated separately
    from the coding region start.  Note that upstream files are 
    generated only when an assembly is released. Therefore, the
    data may be slightly out of synch with the RefSeq data in
    assemblies that are incrementally updated nightly.

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

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

xenoMrna.fa.gz - GenBank mRNA from species other than that of the genome,
    updated once a week via automatic GenBank updates.

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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/mm6/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/mm6/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/mm6/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping \
	'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm6/bigZips/*'
With wget, a single file:
    wget --timestamping \
	'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm6/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 the tables in this directory are freely usable for any purpose. 

This file last updated: 2005-03-15 - 03 March 2005