This directory contains the Build 36 "essentially finished" mouse genome
(UCSC mm8, February 2006) from the Mouse Genome Sequencing Consortium. This
assembly was produced at NCBI.
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.
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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/mm8/chromosomes. To download multiple
files, 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/mm8/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/chrM.fa.gz' \
-O chrM.fa.gz
To unpack the fa.gz files:
gunzip <file>.fa.gz
All the files in this directory are freely available for public use.
This file last updated: 2006-02-16 - 16 February 2006
Name Last modified Size Description
Parent Directory -
chr1.fa.gz 2006-02-16 10:17 60M
chr2.fa.gz 2006-02-16 10:17 56M
chrX.fa.gz 2006-02-16 10:19 50M
chr3.fa.gz 2006-02-16 10:17 49M
chr4.fa.gz 2006-02-16 10:17 47M
chr5.fa.gz 2006-02-16 10:18 46M
chr6.fa.gz 2006-02-16 10:18 46M
chr7.fa.gz 2006-02-16 10:18 44M
chr10.fa.gz 2006-02-16 10:19 40M
chr8.fa.gz 2006-02-16 10:18 39M
chr9.fa.gz 2006-02-16 10:18 38M
chr14.fa.gz 2006-02-16 10:19 38M
chr11.fa.gz 2006-02-16 10:19 37M
chr12.fa.gz 2006-02-16 10:19 36M
chr13.fa.gz 2006-02-16 10:19 36M
chr15.fa.gz 2006-02-16 10:20 31M
chr16.fa.gz 2006-02-16 10:20 30M
chr17.fa.gz 2006-02-16 10:20 29M
chr18.fa.gz 2006-02-16 10:20 27M
chr19.fa.gz 2006-02-16 10:20 18M
chrY_random.fa.gz 2006-02-16 10:20 4.1M
chrY.fa.gz 2006-02-16 10:19 824K
chr5_random.fa.gz 2006-02-16 10:20 824K
chrUn_random.fa.gz 2006-02-16 10:20 217K
chr13_random.fa.gz 2006-02-16 10:20 125K
chr8_random.fa.gz 2006-02-16 10:20 67K
chr7_random.fa.gz 2006-02-16 10:20 33K
chr1_random.fa.gz 2006-02-16 10:20 25K
chr15_random.fa.gz 2006-02-16 10:20 19K
chr17_random.fa.gz 2006-02-16 10:20 14K
chrX_random.fa.gz 2006-02-16 10:20 13K
chr9_random.fa.gz 2006-02-16 10:20 5.9K
chrM.fa.gz 2006-02-16 10:18 5.3K
chr10_random.fa.gz 2006-02-16 10:20 3.7K
md5sum.txt 2006-02-16 12:36 1.6K