This directory contains the Jul. 2004 dog genome assembly from the Broad Institute at MIT (UCSC version canFam1). Files included in this directory: canFam1.2bit - contains the complete dog/canFam1 genome sequence in the 2bit file format. While we are providing the .2bit for this assembly, we will continue to use the .nib files in the Genome Browser. 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.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html chromAgp.zip - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.zip - 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. RepeatMasker March 2004 version with RepBase libraries: RepBase Update 8.12, RM database version 20040306. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per chromosomes. est.fa.gz - Dog ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - Dog 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. 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. ------------------------------------------------------------- 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/canFam1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite the following publication when using these data: Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438:803-19.
Name Last modified Size Description
Parent Directory - canFam1.2bit 2004-07-07 14:39 630M canFam1.chrom.sizes 2004-07-07 05:43 603 canFam1.fa.gz 2020-01-23 02:20 741M chromAgp.zip 2004-07-07 15:55 1.5M chromFa.zip 2004-07-07 16:20 740M chromFaMasked.zip 2004-07-07 16:36 476M chromOut.zip 2004-07-07 15:57 127M chromTrf.zip 2004-07-07 16:36 8.3M est.fa.gz 2019-10-16 21:08 73M est.fa.gz.md5 2019-10-16 21:08 44 md5sum.txt 2014-05-05 16:08 329 mrna.fa.gz 2019-10-16 21:03 1.2M mrna.fa.gz.md5 2019-10-16 21:03 45 refMrna.fa.gz 2019-10-16 21:09 1.1M refMrna.fa.gz.md5 2019-10-16 21:09 48 upstream1000.fa.gz 2019-10-16 21:09 1.5M upstream1000.fa.gz.md5 2019-10-16 21:09 53 upstream2000.fa.gz 2019-10-16 21:09 2.9M upstream2000.fa.gz.md5 2019-10-16 21:09 53 upstream5000.fa.gz 2019-10-16 21:09 7.1M upstream5000.fa.gz.md5 2019-10-16 21:09 53 xenoMrna.fa.gz 2016-03-14 00:50 5.0G xenoMrna.fa.gz.md5 2016-03-14 00:50 49 xenoRefMrna.fa.gz 2019-10-16 21:08 330M xenoRefMrna.fa.gz.md5 2019-10-16 21:08 52