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:
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. RepeatMasker 2006-01-20 (open-3-1-3) version
with RepBase libraries: RM database version 20060120
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 file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed file per chromosome.
mm8.2bit - contains the complete mm8 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
md5sum.txt - MD5 checksum of these files to verify correct transmission
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
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
mm8.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 you use rsync, wget, or ftp rather than downloading the
files via our website. To do so, anonymous ftp to hgdownload.cse.ucsc.edu,
go to the directory goldenPath/mm8/bigZips/.
To download multiple files via ftp, 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
Or with wget, all files:
wget --timestamping \
With wget, a single file:
wget --timestamping \
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To unpack the fa.gz files:
All the tables in this directory are freely usable for any purpose.
This file last updated: 2006-02-16 - 16 February 2006
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80