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 - genes/ 2020-06-19 15:23 - est.fa.gz.md5 2019-10-16 11:33 44 mrna.fa.gz.md5 2019-10-16 11:18 45 refMrna.fa.gz.md5 2019-10-16 11:34 48 xenoMrna.fa.gz.md5 2019-10-16 11:29 49 xenoRefMrna.fa.gz.md5 2019-10-16 11:34 52 upstream1000.fa.gz.md5 2019-10-16 11:34 53 upstream2000.fa.gz.md5 2019-10-16 11:34 53 upstream5000.fa.gz.md5 2019-10-16 11:34 53 monDom5.chrom.sizes 2008-11-25 14:29 161 monDom5.chromAlias.txt 2022-09-08 22:29 332 md5sum.txt 2010-11-09 15:11 361 upstream1000.fa.gz 2019-10-16 11:34 21K monDom5.chromAlias.bb 2022-09-08 22:29 37K upstream2000.fa.gz 2019-10-16 11:34 40K est.fa.gz 2019-10-16 11:33 50K upstream5000.fa.gz 2019-10-16 11:34 97K refMrna.fa.gz 2019-10-16 11:34 212K mrna.fa.gz 2019-10-16 11:18 224K Monodelphis5.0.agp.gz 2009-06-08 16:19 1.9M chromTrf.tar.gz 2009-06-08 16:08 10M chromOut.tar.gz 2009-06-08 14:05 236M monDom5.quals.fa.gz 2009-06-09 10:46 272M xenoRefMrna.fa.gz 2019-10-16 11:34 331M chromFaMasked.tar.gz 2010-11-09 15:10 527M monDom5.2bit 2008-12-01 10:04 907M chromFa.tar.gz 2010-11-09 15:03 1.1G monDom5.fa.gz 2020-01-23 02:24 1.1G xenoMrna.fa.gz 2019-10-16 11:29 6.8G