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. ------------------------------------------------------------------ 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 ... - 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 .tar.gz To uncompress the fa.gz files: gunzip .fa.gz All the tables in this directory are freely usable for any purpose. This file last updated: 2007-07-26 - 26 July 2007