This directory contains the May 2005 dog genome assembly from the 
Broad Institute at MIT (UCSC version canFam2). 

Files included in this directory:

chromAgp.tar.gz - Description of how the assembly was generated from
     fragments, unpacking to one file per chromosome.  

chromFa.tar.gz - 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.  May 3 2005 (open-3-1-0) version of RepeatMasker;
    RepBase libraries: RepBase Update 9.11, RM database version 20050112.

chromFaMasked.tar.gz - The assembly sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.tar.gz - 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.

canFam2.quals.fa.gz - quality scores in fasta file format

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.

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/canFam2/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.