This directory contains compressed multiple alignments of the
following assemblies to the rat genome (rn4, Nov. 2004):
- mouse (Feb 2006, mm8)
- human (Mar 2006, hg18)
- dog (May 2005, canFam2)
- cow (Mar 2005, bosTau2)
- opossum (Jan 2006, monDom4)
- chicken (Feb 2004, galGal2)
- frog (Oct 2004, xenTro1)
- zebrafish (May 2005, danRer3)
The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the rat genome (rn4/Baylr 3.4, Nov. 2004)
aligned to the assemblies.
Files included in this directory:
- chr*.maf.gz files: each contain all the alignments to that
particular rat chromosome.
- 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
rat, 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 rat; 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 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/rn4/multiz9way. To download
multiple files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
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.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80