This directory contains the Jun. 2020 (GRCm39/mm39) assembly of the
mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)),
as well as repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/52
https://www.ncbi.nlm.nih.gov/genome/assembly/7358741
https://www.ncbi.nlm.nih.gov/bioproject/20689
Files included in this directory:
mm39.fa.gz - "Soft-masked" assembly sequence in one file.
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.
mm39.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
mm39.2bit - contains the complete mouse/mm39 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.soe.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
mm39.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
mm39.agp.gz - Description of how the assembly was generated from
fragments.
mm39.chromFa.tar.gz - gzipped tar file with each chromosome sequence
in a separate file, masked as described above for mm39.fa.gz
To extract the files into a directory: tar xvzf mm39.chromFa.tar.gz
mm39.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker
RepBase library: Dfam_Consensus RELEASE 20181026
CC RepBase RELEASE 20181026; *
mm39.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
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 of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - 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.
mm39.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
hg38.chromAlias.bb - bigBed file for alias sequence names, one line
for each sequence name. The first three columns are the sequence in
BED format, followed by tab-separated alias names.
The .bb file is used by bedToBigBed as a URL to avoid having to download
the entire chromAlias.txt file. From the usage message:
-sizesIsChromAliasBb -- If set, then chrom.sizes file is assumed to be a
chromAlias bigBed file or a URL to a such a file (see above).
More documentation is found here:
https://genomewiki.ucsc.edu/index.php?title=Chrom_Alias
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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.soe.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/mm39/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.soe.ucsc.edu/goldenPath/mm39/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/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
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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Name Last modified Size Description
Parent Directory -
genes/ 2024-03-05 12:15 -
md5sum.txt 2022-09-08 14:13 657
mm39.2bit 2020-07-30 09:03 681M
mm39.agp.gz 2020-09-10 12:18 445K
mm39.chrom.sizes 2020-07-27 12:46 1.3K
mm39.chromAlias.bb 2022-09-08 14:13 72K
mm39.chromAlias.txt 2022-09-08 14:13 3.4K
mm39.chromFa.tar.gz 2020-09-10 15:03 830M
mm39.fa.gz 2020-09-10 12:29 830M
mm39.fa.masked.gz 2020-09-10 12:35 481M
mm39.fa.out.gz 2020-09-10 12:19 161M
mm39.trf.bed.gz 2020-09-10 12:19 19M
upstream1000.fa.gz 2020-09-10 12:36 8.0M
upstream2000.fa.gz 2020-09-10 12:36 15M
upstream5000.fa.gz 2020-09-10 12:36 35M