This directory contains the Jul. 2007 assembly of the mouse genome
(mm9, NCBI Build 37), as well as repeat annotations and GenBank sequences.
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:
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.
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 files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
May 17 2007 (open-3-1-8) version of RepeatMasker,
Repeat Masker library RELEASE 20061006
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
mm9.2bit - contains the complete mm9 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
est.fa.gz - Mouse ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Mouse mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
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.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
mm9.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 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/bigZips. 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromFa.tar.gz' \
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
All the tables in this directory are freely usable for any purpose.
This file last updated: 2007-07-26 - 26 July 2007
Name Last modified Size Description
Parent Directory -
xenoMrna.fa.gz 2019-10-17 12:00 6.5G
mm9.fa.gz 2020-01-23 02:23 820M
chromFa.tar.gz 2007-07-25 10:44 820M
est.fa.gz 2019-10-17 12:06 788M
mm9.2bit 2007-07-21 13:31 680M
chromFaMasked.tar.gz 2007-07-25 10:53 481M
xenoRefMrna.fa.gz 2019-10-17 12:07 287M
mrna.fa.gz 2019-10-17 11:49 261M
chromOut.tar.gz 2007-07-25 10:30 149M
refMrna.fa.gz 2019-10-17 12:07 44M
upstream5000.fa.gz 2019-10-17 12:09 36M
chromTrf.tar.gz 2008-05-07 11:07 17M
upstream2000.fa.gz 2019-10-17 12:08 15M
upstream1000.fa.gz 2019-10-17 12:08 7.8M
chromAgp.tar.gz 2007-07-25 10:29 418K
mm9.chrom.sizes 2007-07-19 14:58 584
md5sum.txt 2008-10-16 11:43 254
upstream5000.fa.gz.md5 2019-10-17 12:09 53
upstream2000.fa.gz.md5 2019-10-17 12:08 53
upstream1000.fa.gz.md5 2019-10-17 12:08 53
xenoRefMrna.fa.gz.md5 2019-10-17 12:07 52
xenoMrna.fa.gz.md5 2019-10-17 12:00 49
refMrna.fa.gz.md5 2019-10-17 12:07 48
mrna.fa.gz.md5 2019-10-17 11:49 45
est.fa.gz.md5 2019-10-17 12:06 44
genes/ 2020-02-05 13:47 -