This directory contains alignments of the D. melanogaster assembly
(dm1, Jan. 2003, BDGP Release 3) to the D. virilis assembly (droVir1,
Agencourt 12 July 2004).
Files included in this directory:
- md5sum.txt: checksums for the files in this directory.
- 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 species and the best D. melanogaster match to any part of the
D. virilis genome. The net format is described in
- melanogasterNet.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.
The alignments in melanogasterNet are in "axt" format. For a description,
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 10,000,000 base chunks with 10000 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/droVir1/vsDm1/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The D. virilis data have been freely provided by Agencourt Bioscience
Corporation before publication for use in the UCSC Genome Browser with the
1. The data may be freely downloaded, used in analyses, and repackaged in
2. Users are free to use the data in scientific papers analyzing particular
genes and regions, provided that the Agencourt is properly acknowledged.
3. Agencourt reserves the right to publish the initial large-scale analyses
of the dataset, including large-scale identification of regions of
evolutionary conservation and large-scale genomic assembly.
4. Any redistribution of the data should carry this notice.
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