This directory contains the Sep. 2011 (Broad CanFam3.1/canFam3) assembly of
the dog genome (canFam3, Broad CanFam3.1 (GCA_000002285.2)), as well as
repeat annotations and GenBank sequences.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/85
http://www.ncbi.nlm.nih.gov/genome/assembly/317138
http://www.ncbi.nlm.nih.gov/bioproject/13179
Files included in this directory:
canFam3.2bit - contains the complete dog/canFam3 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.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
canFam3.agp.gz - Description of how the assembly was generated from
fragments.
canFam3.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.
canFam3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
canFam3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. Repeat Masker version: April 26 2011 (open-3-3-0)
database version: RELEASE 20110920
canFam3.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 - Dog 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 - 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.
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.
canFam3.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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/canFam3/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/canFam3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/canFam3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/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 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.
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Name Last modified Size Description
Parent Directory -
est.fa.gz.md5 14-Jul-2017 20:53 44
mrna.fa.gz.md5 14-Jul-2017 20:34 45
refMrna.fa.gz.md5 14-Jul-2017 20:54 48
xenoMrna.fa.gz.md5 14-Jul-2017 20:47 49
xenoRefMrna.fa.gz.md5 14-Jul-2017 20:54 52
upstream1000.fa.gz.md5 14-Jul-2017 20:54 53
upstream2000.fa.gz.md5 14-Jul-2017 20:54 53
upstream5000.fa.gz.md5 14-Jul-2017 20:54 53
md5sum.txt 11-May-2012 09:35 463
canFam3.chrom.sizes 05-Jan-2012 14:52 74K
canFam3.agp.gz 11-May-2012 09:11 148K
upstream1000.fa.gz 14-Jul-2017 20:54 351K
upstream2000.fa.gz 14-Jul-2017 20:54 675K
refMrna.fa.gz 14-Jul-2017 20:54 1.1M
mrna.fa.gz 14-Jul-2017 20:34 1.1M
upstream5000.fa.gz 14-Jul-2017 20:54 1.6M
canFam3.trf.bed.gz 11-May-2012 09:12 9.6M
est.fa.gz 14-Jul-2017 20:53 73M
canFam3.fa.out.gz 11-May-2012 09:12 143M
xenoRefMrna.fa.gz 14-Jul-2017 20:54 300M
canFam3.fa.masked.gz 11-May-2012 09:33 448M
canFam3.2bit 06-Jan-2012 08:49 603M
canFam3.fa.gz 11-May-2012 09:25 747M
xenoMrna.fa.gz 14-Jul-2017 20:46 6.1G