Xenopus tropicalis
Photo courtesy of UNC Chapel Hill, (Chris Showell, all rights reserved.)

The August 2005 frog (Xenopus tropicalis) whole genome shotgun (WGS) assembly version 4.1 was sequenced and assembled by the DOE Joint Genome Institute (JGI).

Sample position queries

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

   Genome Browser Response:

scaffold_3 Displays all of scaffold 3
scaffold_3:1-2000000 Displays first 2 million bases of scaffold_3
scaffold_3:100000+2000 Displays a region of scaffold_3 that spans 2000 bases, starting with position 100000
CR848332 Displays location of mRNA with GenBank accession CR848332
AL680330 Displays location of EST with GenBank accession AL680330
scaffold_1001.7 Displays location of Genscan gene prediction with identifier scaffold_1001.7

dazl Lists dazl mRNAs
zinc finger Lists zinc finger mRNAs
asashima Lists mRNAs deposited by scientists named Asashima
Papalopulu,N. Lists mRNAs deposited by co-author N. Papalopulu

Use this last format for author queries. Although GenBank requires the search format Papalopulu N, internally it uses the format Papalopulu,N..

Assembly Details

Assembly version 4.1--which was constructed from WGS reads using the JGI assembler, Jazz--contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half the genome is contained in 272 scaffolds, each of at least 1.56 Mb in length. In this release, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed by the JGI and placed in a separate directory. The X. tropicalis assembly will be improved over the coming year by additional sequencing of large insert clones, targeted gap closure, and the incorporation of physical and genetic mapping information as it becomes available. For more information about this assembly, see the JGI X. tropicalis website.

The xenTro2 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 JGI and the other institutions who contributed to the sequencing and mapping effort for this release. The xenTro2 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 this release.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.