This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg18, Mar. 2006) aligned to the 
following assemblies:

    _ Human           Homo sapiens                   Mar. 2006   hg18
    _ Chimp           Pan troglodytes                Mar. 2006   panTro2
    _ Gorilla         Gorilla gorilla gorilla        Oct. 2008   gorGor1
    _ Orangutan       Pongo pygmaeus abelii          July 2007   ponAbe2
    _ Rhesus          Macaca mulatta                 Jan. 2006   rheMac2
    _ Marmoset        Callithrix jacchus             June 2007   calJac1
    _ Tarsier         Tarsius syrichta               Aug. 2008   tarSyr1
    _ Mouse lemur     Microcebus murinus             Jun. 2003   micMur1
    _ Bushbaby        Otolemur garnettii             Dec. 2006   otoGar1
    _ TreeShrew       Tupaia belangeri               Dec. 2006   tupBel1
    _ Mouse           Mus musculus                   July 2007   mm9
    _ Rat             Rattus norvegicus              Nov. 2004   rn4
    _ Kangaroo rat    Dipodomys ordii                July 2008   dipOrd1
    _ Guinea Pig      Cavia porcellus                Feb. 2008   cavPor3
    _ Squirrel        Spermophilus tridecemlineatus  Feb. 2008   speTri1
    _ Rabbit          Oryctolagus cuniculus          May  2005   oryCun1
    _ Pika            Ochotona princeps              July 2008   ochPri2
    _ Alpaca          Vicugna pacos                  July 2008   vicPac1
    _ Dolphin         Tursiops truncatus             Feb. 2008   turTru1
    _ Cow             Bos taurus                     Oct. 2007   bosTau4
    _ Horse           Equus caballus                 Sep. 2007   equCab2
    _ Cat             Felis catus                    Mar. 2006   felCat3
    _ Dog             Canis lupus familiaris         May  2005   canFam2
    _ Microbat        Myotis lucifugus               Mar. 2006   myoLuc1
    _ Megabat         Pteropus vampyrus              July 2008   pteVam1
    _ Hedgehog        Erinaceus europaeus            June 2006   eriEur1
    _ Shrew           Sorex araneus                  June 2006   sorAra1
    _ Elephant        Loxodonta africana             July 2008   loxAfr2
    _ Rock hyrax      Procavia capensis              July 2008   proCap1
    _ Tenrec          Echinops telfairi              July 2005   echTel1
    _ Armadillo       Dasypus novemcinctus           July 2008   dasNov2
    _ Sloth           Choloepus hoffmanni            July 2008   choHof1
    _ Opossum         Monodelphis domestica          Jan. 2006   monDom4
    _ Platypus        Ornithorhynchus anatinus       Mar. 2007   ornAna1
    _ Chicken         Gallus gallus                  May  2006   galGal3
    _ Zebra finch     Taeniopygia guttata            July 2008   taeGut1
    _ Lizard          Anolis carolinensis            Feb. 2007   anoCar1
    _ X. tropicalis   Xenopus tropicalis             Aug. 2005   xenTro2
    _ Tetraodon       Tetraodon nigroviridis         Feb. 2004   tetNig1
    _ Fugu            Takifugu rubripes              Oct. 2004   fr2
    _ Stickleback     Gasterosteus aculeatus         Feb. 2006   gasAcu1
    _ Medaka          Oryzias latipes                Oct. 2005   oryLat2
    _ Zebrafish       Danio rerio                    July 2007   danRer5
    _ Lamprey         Petromyzon marinus             Mar. 2007   petMar1

Files included in this directory:
  - knownGene.exon*.fa.gz: for each exon in the hg18 UCSC Gene track, this
    file contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the
    aligning genomes.
  - knownCanonical.exon*.fa.gz: for each exon in the hg18 canonical set of UCSC 
    Genes, this file contains either amino acids (AA) or nucleotides (Nuc) 
    for hg18 and the aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the hg18 RefSeq Gene track, this file 
    contains either amino acids (AA) or nucleotides (Nuc) for hg18 and the 
    aligning genomes.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html
and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.

---------------------------------------------------------------
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 hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/multiz44way/alignments

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

---------------------------------------------------------------
All the files in this directory are freely usable for any 
purpose. For data use restrictions regarding the individual 
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt23-Feb-2011 13:57 4.9K 
[   ]knownCanonical.exonAA.fa.gz07-Dec-2008 18:08 189M 
[   ]knownCanonical.exonNuc.fa.gz07-Dec-2008 18:08 310M 
[   ]knownGene.exonAA.fa.gz07-Dec-2008 18:08 432M 
[   ]knownGene.exonNuc.fa.gz07-Dec-2008 18:08 749M 
[TXT]md5sum.txt13-Jan-2009 09:41 351  
[   ]refGene.exonAA.fa.gz07-Dec-2008 18:09 258M 
[   ]refGene.exonNuc.fa.gz07-Dec-2008 18:09 435M 

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