This directory contains compressed multiple alignments of the
following assemblies to the D. melanogaster genome
(dm3, Apr. 2006, BDGP Release 5)
- D. simulans (droSim1, Apr. 2005)
- D. sechellia (droSec1, Oct. 2005)
- D. yakuba (droYak2, Nov. 2005)
- D. erecta (droEre2, Feb. 2006)
- D. ananassae (droAna3, Feb. 2006)
- D. pseudoobscura (dp4, Feb. 2006)
- D. persimilis (droPer1, Oct. 2005)
- D. willistoni (droWil1, Feb. 2006)
- D. virilis (droVir3, Feb. 2006)
- D. mojavensis (droMoj3, Feb. 2006)
- D. grimshawi (droGri2, Feb. 2006)
- A. gambiae (anoGam1, Feb. 2003)
- A. mellifera (apiMel3, May 2005)
- T. castaneum (triCas2, Sep. 2005)
Files included in this directory:
- chr*.maf.gz files: each contain all the alignments to that
particular D. melanogaster chromosome.
- The maf/upstream*.maf.gz files contain alignments in regions
upstream of annotated transcription starts for FlyBase 5.12 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 D. melanogaster, 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 D. melanogaster;
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.
For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
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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/dm3/multiz15way
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.
Name Last modified Size Description
Parent Directory -
alignments/ 2011-02-23 17:23 -
maf/ 2019-11-06 10:49 -
md5sum.txt 2008-10-27 14:07 895
chrM.maf.gz 2006-12-11 15:55 84K
chrXHet.maf.gz 2006-12-11 15:57 1.1M
chrYHet.maf.gz 2006-12-11 15:57 1.2M
chr2LHet.maf.gz 2006-12-11 15:51 1.8M
chr4.maf.gz 2006-12-11 15:55 7.3M
chr3RHet.maf.gz 2006-12-11 15:55 13M
chr3LHet.maf.gz 2006-12-11 15:53 14M
chr2RHet.maf.gz 2006-12-11 15:52 15M
chrU.maf.gz 2006-12-11 15:55 38M
chrUextra.maf.gz 2006-12-11 15:56 86M
chr2R.maf.gz 2006-12-11 15:52 92M
chrX.maf.gz 2006-12-11 15:57 94M
chr2L.maf.gz 2006-12-11 15:51 102M
chr3L.maf.gz 2006-12-11 15:53 107M
chr3R.maf.gz 2006-12-11 15:55 118M