This directory contains the Jul. 2007 assembly of the mouse genome
(mm9, NCBI Build 37), as well as repeat annotations and GenBank sequences.

This assembly was produced by the Mouse Genome Sequencing Consortium,
and the National Center for Biotechnology Information (NCBI).
See also: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=10090

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.

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 files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    May 17 2007 (open-3-1-8) version of RepeatMasker,
    Repeat Masker library RELEASE 20061006

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format (one file per chromosome).

mm9.2bit - contains the complete mm9 Mouse Genome
    in the 2bit format.  A utility program, twoBitToFa (available
    from our src 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

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 - Mouse 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.

mm9.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

------------------------------------------------------------------
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/mm9/bigZips. To download multiple 
files, use the "mget" command:

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

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz' \
        -O chromFa.tar.gz

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

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

This file last updated: 2007-07-26 - 26 July 2007
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 4.0K 
[   ]chromAgp.tar.gz25-Jul-2007 10:29 418K 
[   ]chromFa.tar.gz25-Jul-2007 10:44 820M 
[   ]chromFaMasked.tar.gz25-Jul-2007 10:53 481M 
[   ]chromOut.tar.gz25-Jul-2007 10:30 149M 
[   ]chromTrf.tar.gz07-May-2008 11:07 17M 
[TXT]md5sum.txt16-Oct-2008 11:43 254  
[   ]mm9.2bit21-Jul-2007 13:31 680M 
[   ]mm9.chrom.sizes19-Jul-2007 14:58 584  
[   ]upstream1000.fa.gz25-Jul-2007 11:12 5.6M 
[   ]upstream2000.fa.gz25-Jul-2007 11:13 11M 
[   ]upstream5000.fa.gz25-Jul-2007 11:15 26M 

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