This directory contains the Build 35 assembly of the mouse genome
(UCSC mm7, August 2005) from the Mouse Genome Sequencing Consortium. This
assembly was produced at NCBI.
Files included in this directory:
mm7.2bit - contains the complete mouse/mm7 genome sequence
in the 2bit file format. 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. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
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 January 12 2005 version with RepBase
libraries: RepBase Update 9.11, RM database version 20050112
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.
mrna.fa.gz - Mouse mRNA from GenBank, updated once a week via automatic
GenBank updates.
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
assemblies.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
mm7.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/mm7/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/mm7/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm7/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm7/bigZips/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm7/bigZips/chromFa.tar.gz' \
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To unpack the fa.gz files:
gunzip <file>.fa.gz
All the tables in this directory are freely usable for any purpose.
This file last updated: 2005-09-20 - 29 September 2005
Name Last modified Size Description
Parent Directory -
chromAgp.tar.gz 2005-09-20 10:13 1.0M
chromFa.tar.gz 2005-09-20 10:56 810M
chromFaMasked.tar.gz 2005-09-20 11:26 488M
chromOut.tar.gz 2005-09-20 11:47 141M
chromTrf.tar.gz 2005-09-20 11:54 17M
est.fa.gz 2019-10-17 13:52 788M
est.fa.gz.md5 2019-10-17 13:52 44
md5sum.txt 2014-01-03 16:53 297
mm7.2bit 2005-08-29 12:29 708M
mm7.chrom.sizes 2005-08-26 12:13 713
mm7.fa.gz 2020-01-23 02:23 811M
mrna.fa.gz 2019-10-17 13:35 261M
mrna.fa.gz.md5 2019-10-17 13:35 45
refMrna.fa.gz 2019-10-17 13:53 44M
refMrna.fa.gz.md5 2019-10-17 13:53 48
upstream1000.fa.gz 2019-10-17 13:53 7.8M
upstream1000.fa.gz.md5 2019-10-17 13:53 53
upstream2000.fa.gz 2019-10-17 13:54 15M
upstream2000.fa.gz.md5 2019-10-17 13:54 53
upstream5000.fa.gz 2019-10-17 13:54 36M
upstream5000.fa.gz.md5 2019-10-17 13:54 53
xenoMrna.fa.gz 2019-10-17 13:45 6.5G
xenoMrna.fa.gz.md5 2019-10-17 13:45 49
xenoRefMrna.fa.gz 2019-10-17 13:52 287M
xenoRefMrna.fa.gz.md5 2019-10-17 13:52 52