This directory contains alignments of the Jan. 2003 D. melanogaster
assembly (dm1, BDGP Release 3.1) to the Jul. 2004 A. mellifera assembly
(apiMel1, BCM HGSC Amel_1.2).
Files included in this directory:
- melanogasterNet.axt.gz: contains chained and netted
alignments, i.e. the best chains in the genome, with gaps in the
best chains filled in by next-best chains where possible.
- melanogaster.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- melanogaster.net.gz: "net" file that describes rearrangements between
the fruitflies and the best D. melanogaster match to any part of the
A. mellifera genome. The net format is described in
- md5sum.txt: checksums of the files in this directory
The alignments in the melanogasterNet.axt.gz file are in "axt" format.
For a description, see http://genome.ucsc.edu/goldenPath/help/axt.html.
The alignments were produced by the blastz alignment program, which
is available from Webb Miller's lab at Penn State University
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 91
with a gap open penalty of 400 and a gap extension penalty of 30. The
minimum score for an alignment to be kept was 3000 for the first pass
and 2200 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.
Each chromosome was divided into 10,010,000 base chunks with 10,000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt.
The axtNet alignments were processed with chainNet, netSyntenic,
and netClass written by Jim Kent at UCSC.
If you plan to download a large file or multiple files from this
directory, we recommend 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/apiMel1/vsDm1/. 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 available for public use.
For conditions of use regarding the A. mellifera sequence data, see
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80