This directory contains the Mar. 2007 assembly of the platypus genome
(ornAna1, WUSTL version 5.0.1), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the
Washington University School of Medicine in St. Louis.
For more information on the platypus genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Ornithorhynchus%20anatinus
Files included in this directory:
ornAna1.2bit - contains the complete platypus/ornAna1 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
ornAna1.agp.gz - Description of how the assembly was generated from
fragments.
ornAna1.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
ornAna1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
ornAna1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. The May 17 2007 (open-3-1-8) version of
RepeatMasker was used with the 20070717 (under development) library
from RepBase Update.
ornAna1.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
ornAna1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Platypus mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
ornAna1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
ornAna1.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
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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/ornAna1/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The Platypus sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing these data
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.
Name Last modified Size Description
Parent Directory -
est.fa.gz 2019-10-17 14:52 1.8M
est.fa.gz.md5 2019-10-17 14:52 44
genes/ 2020-02-05 13:47 -
md5sum.txt 2014-01-03 16:10 358
mrna.fa.gz 2019-10-17 14:38 70K
mrna.fa.gz.md5 2019-10-17 14:38 45
ornAna1.2bit 2007-07-24 12:03 514M
ornAna1.agp.gz 2007-07-24 12:14 7.9M
ornAna1.chrom.sizes 2007-02-05 16:25 3.3M
ornAna1.chromAlias.bb 2022-09-08 14:14 59M
ornAna1.chromAlias.txt 2022-09-08 14:14 10M
ornAna1.fa.gz 2007-07-24 12:25 577M
ornAna1.fa.masked.gz 2007-07-24 12:32 328M
ornAna1.fa.out.gz 2007-07-24 12:15 147M
ornAna1.quals.fa.gz 2009-06-09 10:42 430M
ornAna1.trf.bed.gz 2007-07-24 12:15 2.4M
refMrna.fa.gz 2019-10-17 14:52 155K
refMrna.fa.gz.md5 2019-10-17 14:52 48
upstream1000.fa.gz 2019-10-17 14:53 2.2M
upstream1000.fa.gz.md5 2019-10-17 14:53 53
upstream2000.fa.gz 2019-10-17 14:54 4.0M
upstream2000.fa.gz.md5 2019-10-17 14:54 53
upstream5000.fa.gz 2019-10-17 14:55 8.6M
upstream5000.fa.gz.md5 2019-10-17 14:55 53
xenoMrna.fa.gz 2019-10-17 14:47 6.8G
xenoMrna.fa.gz.md5 2019-10-17 14:48 49
xenoRefMrna.fa.gz 2019-10-17 14:52 331M
xenoRefMrna.fa.gz.md5 2019-10-17 14:52 52