This directory contains the Monodelphis domestica genome
(UCSC monDom4, January 2006) from The Broad Institute.
Files included in this directory:
Monodelphis4.0.agp.gz - Description of how the assembly was generated from
fragments.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
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. Repeat Masker database version: 20060120
chromFaMasked.tar.gz - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed file per chromosome.
monDom4.2bit - contains the complete monDom4 Opossum Genome
in the 2bit format. A utility program, twoBitToFa (available
from our src tree), can be used to extract .fa file(s) from
this file. See also:
http://genome.ucsc.edu/admin/cvs.html - CVS access to the source tree
http://genome.ucsc.edu/admin/jk-install.html - building the utilities
monDom4.quals.fa.gz - quality scores in fasta file format
md5sum.txt - MD5 checksum of these files to verify correct transmission
monDom4.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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If you plan to download a large file or multiple files from this directory,
we recommend you use rsync, wget, or ftp rather than downloading the
files via our website. To do so, anonymous ftp to hgdownload.cse.ucsc.edu,
go to the directory goldenPath/monDom4/bigZips/.
To download multiple files via ftp, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/chromFa.tar.gz' \
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To unpack the fa.gz files:
gunzip <file>.fa.gz
All the files in this directory are freely usable for any purpose.
This file last updated: 2009-06-10 - 10 June 2009
Name Last modified Size Description
Parent Directory -
xenoRefMrna.fa.gz.md5 2019-10-17 14:23 52
xenoRefMrna.fa.gz 2019-10-17 14:23 331M
xenoMrna.fa.gz.md5 2016-03-16 09:03 49
xenoMrna.fa.gz 2016-03-16 09:03 5.0G
upstream5000.fa.gz.md5 2019-10-17 14:23 53
upstream5000.fa.gz 2019-10-17 14:23 2.2M
upstream2000.fa.gz.md5 2019-10-17 14:23 53
upstream2000.fa.gz 2019-10-17 14:23 955K
upstream1000.fa.gz.md5 2019-10-17 14:23 53
upstream1000.fa.gz 2019-10-17 14:23 502K
refMrna.fa.gz.md5 2019-10-17 14:23 48
refMrna.fa.gz 2019-10-17 14:23 212K
mrna.fa.gz.md5 2019-10-17 14:18 45
mrna.fa.gz 2019-10-17 14:18 224K
monDom4.quals.fa.gz 2009-06-09 10:46 272M
monDom4.fa.gz 2020-01-23 02:24 1.1G
monDom4.chrom.sizes 2006-02-09 16:08 150
monDom4.2bit 2006-02-11 23:15 906M
md5sum.txt 2009-06-10 10:24 406
est.fa.gz.md5 2019-10-17 14:22 44
est.fa.gz 2019-10-17 14:22 50K
chromTrf.tar.gz 2006-05-15 12:09 9.2M
chromOut.tar.gz 2006-05-15 12:02 220M
chromFaMasked.tar.gz 2006-05-15 12:00 531M
chromFa.tar.gz 2006-05-15 11:46 1.1G
Monodelphis4.0.agp.gz 2006-05-15 11:28 1.9M