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. ------------------------------------------------------------------ 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.txt 2020-09-29 10:49 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