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