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 ------------------------------------------------------------------ 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 ... - 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 .tar.gz To uncompress the fa.gz files: gunzip .fa.gz ----------------------------------------------------------------------------- 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. -----------------------------------------------------------------------------