This directory contains zipped multiple alignments of the following
genomes to the Human genome (hg16, Jul. 2003):
- Chimp (panTro1, Nov. 2003)
- Mouse (mm3, Feb. 2003)
- Rat (rn3, Jun. 2003)
- Chicken (galGal2, Feb. 2004)
The chr*.maf.gz files each contain all the alignments to
that particular human chromosome.
The pt1, mm3, rn3, and gg2 directories contained gzipped mafs
for the pairwise (blastz) alignments used in the multiple alignment.
The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for RefSeq genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in
human, whether or not alignments actually exist. In situations where no
alignments exist or the alignments of one or more species are missing,
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in human; therefore, only the
species name is displayed in the alignment data and no position information
is recorded. The alignment score is always zero in these files. These files
are updated weekly.
For a description of the multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
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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/hg16/mzPt1Mm3Rn3Gg2. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All files in this directory are freely available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
rn3/ 2004-04-23 09:00 -
pt1/ 2004-04-23 09:00 -
mm3/ 2004-04-23 09:00 -
gg2/ 2004-04-23 09:00 -
chr19_random.maf.gz 2004-03-11 10:23 4.9K
chr2.maf.gz 2004-03-11 10:09 168M
chr3.maf.gz 2004-03-11 10:08 139M
chr5.maf.gz 2004-03-11 10:08 125M
chr6.maf.gz 2004-03-11 10:08 117M
chr7.maf.gz 2004-03-11 10:08 106M
chr4.maf.gz 2004-03-11 10:07 127M
chr9.maf.gz 2004-03-11 10:07 81M
chr8.maf.gz 2004-03-11 10:07 98M
chrX.maf.gz 2004-03-11 10:07 81M
chr17.maf.gz 2004-03-11 10:06 56M
chr16.maf.gz 2004-03-11 10:06 56M
chr18.maf.gz 2004-03-11 10:06 52M
chr19.maf.gz 2004-03-11 10:05 33M
chr20.maf.gz 2004-03-11 10:05 42M
chrY.maf.gz 2004-03-11 10:04 7.0M
chrX_random.maf.gz 2004-03-11 10:04 885K
chr22.maf.gz 2004-03-11 10:04 23M
chr21.maf.gz 2004-03-11 10:04 22M
chrUn_random.maf.gz 2004-03-11 10:03 1.4M
chrM.maf.gz 2004-03-11 10:03 27K
chr9_random.maf.gz 2004-03-11 10:03 887K
chr8_random.maf.gz 2004-03-11 10:03 287K
chr7_random.maf.gz 2004-03-11 10:03 173K
chr6_random.maf.gz 2004-03-11 10:03 813K
chr5_random.maf.gz 2004-03-11 10:02 37K
chr4_random.maf.gz 2004-03-11 10:02 161K
chr1_random.maf.gz 2004-03-11 10:02 2.1M
chr18_random.maf.gz 2004-03-11 10:02 3.3K
chr17_random.maf.gz 2004-03-11 10:02 657K
chr3_random.maf.gz 2004-03-11 10:02 358K
chr2_random.maf.gz 2004-03-11 10:02 201K
chr1.maf.gz 2004-03-11 09:47 157M
chr11.maf.gz 2004-03-11 09:46 94M
chr10.maf.gz 2004-03-11 09:46 93M
chr12.maf.gz 2004-03-11 09:46 90M
chr15.maf.gz 2004-03-11 09:46 59M
chr14.maf.gz 2004-03-11 09:46 62M
chr13.maf.gz 2004-03-11 09:45 65M
chr15_random.maf.gz 2004-03-11 09:44 414K
chr10_random.maf.gz 2004-03-11 09:43 495K
chr13_random.maf.gz 2004-03-11 09:43 92K