This directory contains compressed multiple alignments of the
following assemblies to the Lancelet genome (braFlo1, Mar 2006):
- lancelet Branchiostoma floridae Mar 2006, braFlo1 reference
- human Homo sapiens Mar 2006, hg18 recip best net
- mouse Mus musculus July 2007, mm9 recip best net
- chicken Gallus gallus May 2006, galGal3 recip best net
- lamprey Petromyzon marinus June 2007, petMar1 recip best net
These alignments were prepared using the methods described in the
track description file, multiz5way.html, based on the
phylogenetic tree, 5way.nh.
The braFlo1.5way.maf.gz file contains all the alignments to the
Lancelet contigs, with additional annotations to indicate gap context.
The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Xeno 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
lancelet, 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 lancelet; 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
http://genome.ucsc.edu/goldenPath/help/maf.html.
PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/phastCons5way
---------------------------------------------------------------
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/braFlo1/multiz5way
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.
Checksum values for all files in this directory can be found in md5sum.txt.
Name Last modified Size Description
Parent Directory -
maf/ 2019-11-06 10:38 -
md5sum.txt 2008-10-16 12:15 135
chrUn.maf.gz 2008-04-30 11:30 75M
chrM.maf.gz 2008-04-30 09:29 26K
5way.nh 2008-04-17 12:52 156