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
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.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80