This directory contains the Build 32 assembly of the mouse genome 
(mm4, Oct. 2003) from the Mouse Genome Sequencing Consortium. This 
assembly was produced at NCBI.  

Files included in this directory:

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

chromFa.zip - 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 June 2003 version with RepBase
    libraries: RepBase Update 8.4, RM database version 20030619

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

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

chromTrf.zip - 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.  

contigAgp.zip - Description of how the assembly was generated from
    fragments at a contig layout level. 

contigFa.zip - The assembly sequence contig, in one file per contig.
    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.

contigFaMasked.zip - The assembly sequence contigs, in one file
    per contig. Repeats are masked by capital Ns; non-repeating sequence 
    is shown in upper case.  

contigOut.zip - RepeatMasker .out file for contigs.  These were 
    created by RepeatMasker at the -s sensitive setting.

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one .bed 
    file per contig.  

mrna.zip - Mouse mRNA from GenBank.

refMrna.zip - RefSeq mRNA from the same species as the genome.

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.zip - All GenBank mRNA from species other than that of the genome.

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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/mm4/bigZips. To download 
multiple files, use the "mget" command:

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

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