This directory contains the Apr. 2009 (Broad/oryCun2) assembly of the rabbit genome (oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)), as well as repeat annotations and GenBank sequences. This assembly was produced by the Broad Institute of MIT and Harvard. For more information on the rabbit genome, see the project website: http://www.broadinstitute.org/science/projects/mammals-models/rabbit/rabbit-genome-sequencing-project Files included in this directory: oryCun2.2bit - contains the complete rabbit/oryCun2 genome sequence in the 2bit file format. 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/cvs.html http://genome.ucsc.edu/admin/jk-install.html oryCun2.agp.gz - Description of how the assembly was generated from fragments. oryCun2.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. oryCun2.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. oryCun2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC) oryCun2.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 - Rabbit 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 - Rabbit 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. oryCun2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. oryCun2.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ 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 [username: anonymous, password: your email address], then cd to the directory goldenPath/oryCun2/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/oryCun2/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/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 The Rabbit sequence is made freely available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. 3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. 1. The data may be freely downloaded, used in analyses, and repackaged in databases.
Name Last modified Size Description
Parent Directory - est.fa.gz 2019-10-16 12:53 6.9M est.fa.gz.md5 2019-10-16 12:53 44 genes/ 2020-10-02 13:38 - md5sum.txt 2010-05-20 16:29 510 mrna.fa.gz 2019-10-16 12:37 1.1M mrna.fa.gz.md5 2019-10-16 12:37 45 oryCun2.2bit 2009-08-12 10:39 682M oryCun2.agp.gz 2010-04-02 13:40 2.1M oryCun2.chrom.sizes 2009-08-11 11:46 50K oryCun2.chromAlias.txt 2020-09-29 10:49 67K oryCun2.fa.gz 2010-04-02 13:57 815M oryCun2.fa.masked.gz 2010-04-02 14:08 482M oryCun2.fa.out.gz 2010-04-02 13:41 140M oryCun2.trf.bed.gz 2010-04-02 13:41 8.5M refMrna.fa.gz 2019-10-16 12:53 888K refMrna.fa.gz.md5 2019-10-16 12:53 48 upstream1000.fa.gz 2019-10-16 12:54 14M upstream1000.fa.gz.md5 2019-10-16 12:54 53 upstream2000.fa.gz 2019-10-16 12:55 27M upstream2000.fa.gz.md5 2019-10-16 12:55 53 upstream5000.fa.gz 2019-10-16 12:56 77M upstream5000.fa.gz.md5 2019-10-16 12:56 53 xenoMrna.fa.gz 2019-10-16 12:48 6.8G xenoMrna.fa.gz.md5 2019-10-16 12:48 49 xenoRefMrna.fa.gz 2019-10-16 12:53 330M xenoRefMrna.fa.gz.md5 2019-10-16 12:53 52