This directory contains alignments of the human assembly
(hg17, Jul. 2003) to the chicken assembly (galGal2, Feb. 2004).
Files included in this directory:
- axtChrom directory: contains the axt alignments generated by blastz,
in one file per chromosome. Blastz output was converted to lav format,
which was then converted to axt format.
- human.chain.zip: chained blastz alignments. The chain format is
described in http://genome.ucsc.edu/goldenPath/help/chain.html.
- human.net.zip: "net" file that describes rearrangements between the
species and the best human match to any part of the chicken genome.
The net format is described in
- md5sum.txt: checksums of the files in this directory
The alignments in the axtChrom directory 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 -90 -25 -100
C -90 100 -100 -25
G -25 -100 100 -90
T -100 -25 -90 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 10,000 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 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt.
If you plan 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 to hgdownload.cse.ucsc.edu,
then go to the directory goldenPath/galGal2/vsHg16/. To download
multiple files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The chicken sequence is made freely available before scientific
publication with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the providers of these data are
properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome
(that is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80