Monodelphis domestica Photo courtesy of Paul Samollow, Southwest Foundation for Biomedical Research, San Antonio. (NHGRI Press Photos)

The June 2005 opossum (Monodelphis domestica) V3 preliminary assembly was produced by The Broad Institute.

Sample position queries

A genome position can be specified by a scaffold coordinate range, an mRNA or EST, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the opossum genome. See the User's Guide for more information.

Request:		Genome Browser Response:
scaffold_1802		Displays all of scaffold #1802
scaffold_6606:63,250-84,705		Displays bases 63250 through 84705 of scaffold #6606
AF049761		Displays region of mRNA with GenBank accession number AF049761
CLOCK		Displays region of genome showing tBLASTn alignment of peptides from human CLOCK gene
immunoglobulin		Lists immunoglobulin regions
immunoglobulin light chain kappa		Lists only immunoglobulin light chain kappa mRNAs
miller		Lists mRNAs deposited by scientists named Miller
Miska,K.B.		Lists mRNAs deposited by co-author K.B. Miska

Use this last format for author queries. Although GenBank requires the search format Miska KB, internally it uses the format Miska,K.B.

Assembly Details

The Broad Institute reports the following statistics on the monDom2 assembly:

• Placed reads: 33,507,069
• Number of contigs: 65,946
• Total bases in contigs: 3,496,445,653
• Number of scaffolds: 5,077
• Total bases in scaffolds: 3,575,239,585
• Number of gap bases in scaffolds between contigs: 78,793,932
• GC/AT ratio: 1,322,125,364/2,174,320,289 = 0.6081
• Scaffold names: scaffold_0 - scaffold_5076
• Largest scaffold: scaffold_0 at 199,827,570 bases
• Smallest scaffold: scaffold_5076 at 2,002 bases

The monDom2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use.

Many thanks to The Broad Institute for the opossum assembly data. The monDom2 annotation tracks were generated by UCSC and collaborators worldwide. See the credits page for a detailed list of the organizations and individuals who contributed to the success of this release.