This directory contains the Monodelphis domestica genome
(UCSC monDom5, October 2006) from The Broad Institute.
Files included in this directory:
Monodelphis5.0.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.
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.
monDom5.2bit - contains the complete monDom5 Opossum Genome
in the 2bit format. A utility program, twoBitToFa (available
from our source 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
monDom5.quals.fa.gz - quality scores in fasta file format
est.fa.gz - Mouse ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Opossum mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the RefSeq data which is updated daily for most
assemblies.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
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.
monDom5.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
monDom5.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 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/monDom5/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/monDom5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom5/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 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 -
Monodelphis5.0.agp.gz 2009-06-08 16:19 1.9M
chromFa.tar.gz 2010-11-09 15:03 1.1G
chromFaMasked.tar.gz 2010-11-09 15:10 527M
chromOut.tar.gz 2009-06-08 14:05 236M
chromTrf.tar.gz 2009-06-08 16:08 10M
est.fa.gz 2019-10-16 11:33 50K
est.fa.gz.md5 2019-10-16 11:33 44
genes/ 2020-06-19 15:23 -
md5sum.txt 2010-11-09 15:11 361
monDom5.2bit 2008-12-01 10:04 907M
monDom5.chrom.sizes 2008-11-25 14:29 161
monDom5.chromAlias.bb 2022-09-08 22:29 37K
monDom5.chromAlias.txt 2022-09-08 22:29 332
monDom5.fa.gz 2020-01-23 02:24 1.1G
monDom5.quals.fa.gz 2009-06-09 10:46 272M
mrna.fa.gz 2019-10-16 11:18 224K
mrna.fa.gz.md5 2019-10-16 11:18 45
refMrna.fa.gz 2019-10-16 11:34 212K
refMrna.fa.gz.md5 2019-10-16 11:34 48
upstream1000.fa.gz 2019-10-16 11:34 21K
upstream1000.fa.gz.md5 2019-10-16 11:34 53
upstream2000.fa.gz 2019-10-16 11:34 40K
upstream2000.fa.gz.md5 2019-10-16 11:34 53
upstream5000.fa.gz 2019-10-16 11:34 97K
upstream5000.fa.gz.md5 2019-10-16 11:34 53
xenoMrna.fa.gz 2019-10-16 11:29 6.8G
xenoMrna.fa.gz.md5 2019-10-16 11:29 49
xenoRefMrna.fa.gz 2019-10-16 11:34 331M
xenoRefMrna.fa.gz.md5 2019-10-16 11:34 52