This directory contains the Jul. 2007 assembly of the mouse genome
(mm9, NCBI Build 37) in one gzip-compressed FASTA file per chromosome.

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:

  - 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).

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 chrN_random.fa.gz files contain clones that are not 
yet finished or cannot be placed with certainty at a specific place on 
the chromosome.  The chrUn_random.fa.gz sequence are unfinished clones,
or clones that can not be tenatively placed 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/mm9/chromosomes. 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/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/chrM.fa.gz .

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

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

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

This file last updated: 2007-07-26 - 26 July 2007
      Name                    Last modified      Size  Description
Parent Directory - md5sum.txt 2007-07-25 11:07 1.6K chrY_random.fa.gz 2007-07-25 10:29 17M chrX_random.fa.gz 2007-07-25 10:29 408K chrUn_random.fa.gz 2007-07-25 10:29 1.0M chr9_random.fa.gz 2007-07-25 10:29 125K chr8_random.fa.gz 2007-07-25 10:29 223K chr7_random.fa.gz 2007-07-25 10:29 92K chr5_random.fa.gz 2007-07-25 10:29 98K chr4_random.fa.gz 2007-07-25 10:29 34K chr3_random.fa.gz 2007-07-25 10:29 13K chrY.fa.gz 2007-07-25 10:29 877K chrM.fa.gz 2007-07-25 10:29 5.3K chr17_random.fa.gz 2007-07-25 10:29 169K chr16_random.fa.gz 2007-07-25 10:29 1.4K chr13_random.fa.gz 2007-07-25 10:29 110K chr1_random.fa.gz 2007-07-25 10:29 329K chrX.fa.gz 2007-07-25 10:29 50M chr19.fa.gz 2007-07-25 10:29 18M chr18.fa.gz 2007-07-25 10:28 27M chr17.fa.gz 2007-07-25 10:28 29M chr16.fa.gz 2007-07-25 10:28 30M chr15.fa.gz 2007-07-25 10:28 31M chr14.fa.gz 2007-07-25 10:28 38M chr13.fa.gz 2007-07-25 10:28 36M chr12.fa.gz 2007-07-25 10:28 37M chr11.fa.gz 2007-07-25 10:28 37M chr10.fa.gz 2007-07-25 10:27 40M chr9.fa.gz 2007-07-25 10:27 38M chr8.fa.gz 2007-07-25 10:27 39M chr7.fa.gz 2007-07-25 10:27 44M chr6.fa.gz 2007-07-25 10:27 46M chr5.fa.gz 2007-07-25 10:27 46M chr4.fa.gz 2007-07-25 10:26 47M chr3.fa.gz 2007-07-25 10:26 49M chr2.fa.gz 2007-07-25 10:26 56M chr1.fa.gz 2007-07-25 10:26 60M