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.
canFam3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
canFam3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
canFam3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
canFam3.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/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.
------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
canFam3.2bit 2012-01-06 08:49 603M
canFam3.agp.gz 2012-05-11 09:11 148K
canFam3.chrom.sizes 2012-01-05 14:52 74K
canFam3.chromAlias.bb 2022-09-08 14:10 945K
canFam3.chromAlias.txt 2022-09-08 14:10 192K
canFam3.fa.gz 2012-05-11 09:25 747M
canFam3.fa.masked.gz 2012-05-11 09:33 448M
canFam3.fa.out.gz 2012-05-11 09:12 143M
canFam3.gc5Base.wib 2019-01-17 14:45 458M
canFam3.gc5Base.wig.gz 2019-01-17 14:45 8.9M
canFam3.gc5Base.wigVarStep.gz 2012-01-05 15:22 1.2G
canFam3.trf.bed.gz 2012-05-11 09:12 9.6M
est.fa.gz 2019-10-15 12:38 73M
est.fa.gz.md5 2019-10-15 12:38 44
genes/ 2020-10-02 13:37 -
md5sum.txt 2019-01-17 15:51 638
mrna.fa.gz 2019-10-15 12:23 1.2M
mrna.fa.gz.md5 2019-10-15 12:23 45
refMrna.fa.gz 2019-10-15 12:39 1.1M
refMrna.fa.gz.md5 2019-10-15 12:39 48
upstream1000.fa.gz 2019-10-15 12:39 354K
upstream1000.fa.gz.md5 2019-10-15 12:39 53
upstream2000.fa.gz 2019-10-15 12:39 682K
upstream2000.fa.gz.md5 2019-10-15 12:39 53
upstream5000.fa.gz 2019-10-15 12:39 1.6M
upstream5000.fa.gz.md5 2019-10-15 12:39 53
xenoMrna.fa.gz 2019-10-15 12:33 6.8G
xenoMrna.fa.gz.md5 2019-10-15 12:33 49
xenoRefMrna.fa.gz 2019-10-15 12:39 330M
xenoRefMrna.fa.gz.md5 2019-10-15 12:39 52