This directory contains the Oct. 2004 preliminary assembly of the Monodelphis domestica (South American, Short-tailed Opossum) genome (monDom1, Oct. 2004) from the Broad Institute. Files included in this directory: hardMask.fa.gz - The hard masked file. The assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. md5sum.txt - Checksums for the .gz files in this directory. Excluding mrna.fa.gz and xenoMrna.fa.gz since they change weekly. mrna.fa.gz - GenBank mRNA sequences for Monodelphis domestica. This sequence data is updated once a week via automatic GenBank updates. novel.RM.lib.fa.gz - additional Repeat Masker library representing novel sequences in addition to the standard mammal library repeats. Created by Damian Keefe of Ensembl for the ENCODE project. See also: ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/repeat_libraries/README http://www.nisc.nih.gov/open_page.html?/projects/encode/index.cgi rmsk.sql - SQL structure for database table rmsk (see rmsk.txt.gz) rmsk.txt.gz - text dump of data base table rmsk - see also the SQL structure for this data base table in the file rmsk.sql This is the result from the Repeat Masker operation on the assembly. The -s sensitive setting was used with Repeat Masker and library version: RepBase Update 9.04, RM database version 20040702 softMask.fa.gz - The soft Masked file. The 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. trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file. xenoMrna.fa.gz - All GenBank mRNA sequences except Monodelphis domestica mRNA. This sequence data is updated once a week via automatic GenBank updates. monDom1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------------- 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/monDom1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Preliminary drafts of the opossum sequence are made freely available before scientific publication by the Broad Institute, 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 particular genes and regions if the provider of this data (The Broad Institute) is properly acknowledged. 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 - hardMask.fa.gz 2004-12-07 11:09 582M md5sum.txt 2005-02-18 10:58 242 monDom1.2bit 2004-12-06 15:55 903M monDom1.chrom.sizes 2004-12-03 11:37 374K monDom1.fa.gz 2020-02-05 14:47 1.1G mrna.fa.gz 2020-02-28 12:40 224K mrna.fa.gz.md5 2020-02-28 12:40 45 novel.RM.lib.fa.gz 2004-12-03 15:54 189K rmsk.sql 2005-01-06 16:25 1.1K rmsk.txt.gz 2005-01-06 16:33 446M softMask.fa.gz 2004-12-06 16:49 1.1G trf.bed.gz 2004-12-06 11:23 9.4M xenoMrna.fa.gz 2016-03-16 10:43 5.0G xenoMrna.fa.gz.md5 2016-03-16 10:43 49 xenoRefMrna.fa.gz 2020-02-28 12:40 336M xenoRefMrna.fa.gz.md5 2020-02-28 12:40 52