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.
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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.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.fa.gz 2020-01-23 02:20 741M
upstream5000.fa.gz.md5 2019-10-16 21:09 53
upstream5000.fa.gz 2019-10-16 21:09 7.1M
upstream2000.fa.gz.md5 2019-10-16 21:09 53
upstream2000.fa.gz 2019-10-16 21:09 2.9M
upstream1000.fa.gz.md5 2019-10-16 21:09 53
upstream1000.fa.gz 2019-10-16 21:09 1.5M
refMrna.fa.gz.md5 2019-10-16 21:09 48
refMrna.fa.gz 2019-10-16 21:09 1.1M
xenoRefMrna.fa.gz.md5 2019-10-16 21:08 52
xenoRefMrna.fa.gz 2019-10-16 21:08 330M
est.fa.gz.md5 2019-10-16 21:08 44
est.fa.gz 2019-10-16 21:08 73M
mrna.fa.gz.md5 2019-10-16 21:03 45
mrna.fa.gz 2019-10-16 21:03 1.2M
xenoMrna.fa.gz.md5 2016-03-14 00:50 49
xenoMrna.fa.gz 2016-03-14 00:50 5.0G
md5sum.txt 2014-05-05 16:08 329
chromTrf.zip 2004-07-07 16:36 8.3M
chromFaMasked.zip 2004-07-07 16:36 476M
chromFa.zip 2004-07-07 16:20 740M
chromOut.zip 2004-07-07 15:57 127M
chromAgp.zip 2004-07-07 15:55 1.5M
canFam1.2bit 2004-07-07 14:39 630M
canFam1.chrom.sizes 2004-07-07 05:43 603