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 -
md5sum.txt 16-Feb-2006 12:36 1.6K
chr10_random.fa.gz 16-Feb-2006 10:20 3.7K
chrM.fa.gz 16-Feb-2006 10:18 5.3K
chr9_random.fa.gz 16-Feb-2006 10:20 5.9K
chrX_random.fa.gz 16-Feb-2006 10:20 13K
chr17_random.fa.gz 16-Feb-2006 10:20 14K
chr15_random.fa.gz 16-Feb-2006 10:20 19K
chr1_random.fa.gz 16-Feb-2006 10:20 25K
chr7_random.fa.gz 16-Feb-2006 10:20 33K
chr8_random.fa.gz 16-Feb-2006 10:20 67K
chr13_random.fa.gz 16-Feb-2006 10:20 125K
chrUn_random.fa.gz 16-Feb-2006 10:20 217K
chr5_random.fa.gz 16-Feb-2006 10:20 824K
chrY.fa.gz 16-Feb-2006 10:19 824K
chrY_random.fa.gz 16-Feb-2006 10:20 4.1M
chr19.fa.gz 16-Feb-2006 10:20 18M
chr18.fa.gz 16-Feb-2006 10:20 27M
chr17.fa.gz 16-Feb-2006 10:20 29M
chr16.fa.gz 16-Feb-2006 10:20 30M
chr15.fa.gz 16-Feb-2006 10:20 31M
chr13.fa.gz 16-Feb-2006 10:19 36M
chr12.fa.gz 16-Feb-2006 10:19 36M
chr11.fa.gz 16-Feb-2006 10:19 37M
chr14.fa.gz 16-Feb-2006 10:19 38M
chr9.fa.gz 16-Feb-2006 10:18 38M
chr8.fa.gz 16-Feb-2006 10:18 39M
chr10.fa.gz 16-Feb-2006 10:19 40M
chr7.fa.gz 16-Feb-2006 10:18 44M
chr6.fa.gz 16-Feb-2006 10:18 46M
chr5.fa.gz 16-Feb-2006 10:18 46M
chr4.fa.gz 16-Feb-2006 10:17 47M
chr3.fa.gz 16-Feb-2006 10:17 49M
chrX.fa.gz 16-Feb-2006 10:19 50M
chr2.fa.gz 16-Feb-2006 10:17 56M
chr1.fa.gz 16-Feb-2006 10:17 60M