This directory contains alignments of the following assemblies:
- target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1)
- query: Zebrafish (danRer3, May 2005, Sanger Centre, Danio rerio Sequencing
Files included in this directory:
- md5sum.txt: md5sum checksums for the files in this directory
- hg18.danRer3.all.chain.gz: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html .
- hg18.danRer3.net.gz: "net" file that describes rearrangements between
the species and the best Zebrafish match to any part of the
Human genome. The net format is described in
- axtNet/*.hg18.danRer3.net.axt.gz: chained and netted alignments,
i.e. the best chains in the Human genome, with gaps in the best
chains filled in by next-best chains where possible. The axt format is
described in http://genome.ucsc.edu/goldenPath/help/axt.html .
The hg18 and danRer3 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/). Any hg18 sequences larger
than 10,010,000 bases were split into chunks of 10,010,000 bases overlapping
by 10,000 bases for alignment. A similar process was followed for danRer3,
with chunks of 10,000,000 overlapping by 0. Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State.
Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random
chromosomes are comprised of unordered scaffolds separated by 500 <em>N</em>s
and 1000 <em>N</em>s respectively, the blastz alignments and subsequent
chaining were first performed on the scaffolds, and the coordinates were then
lifted up to the chromosome level. This avoided false alignments across the
<em>N</em>s. Random unordered chromosomes from human were treated in a
similar manner so that alignments were performed using the contigs whcih are
separated by 50000 Ns. For alignments involving zebrafish chrNA and chrUn
scaffolds, lineage-specific repeats were not used, but the M parameter was
set to 50 in order to utilize the Blastz dynamic masking functionality. Each
chunk of human sequence was aligned with all of the zebrafish sequence in
order for dynamic masking to occur.
The blastz scoring matrix (Q parameter) used was:
A C G T
A 91 -90 -25 -100
C -90 100 -100 -25
G -25 -100 100 -90
T -100 -25 -90 91
with a gap open penalty of O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=2200 for the first pass
and L=6000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass. The minimum
score for alignments to be interpolated between was H=2000. Other blastz
parameters specifically set for this species pair:
The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.
Chain minimum score: 5000, and linearGap matrix of (loose):
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were written by Jim Kent at UCSC.
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:
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg18/vsDanRer3
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 files in this directory are freely available for public use.
Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic
sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1), 103-7 (2003).
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