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Resource:Tribolium castaneum Genome Project

Name: Resource:Tribolium castaneum Genome Project
Description:

This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below.
The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University).
Access to the Data

- Genome Assembly:

The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder.
A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page.
The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change.

- BLAST Searches:

The BLAST link is located in the sidebar.

  • Linearized chromosome and unplaced scaffold sequences
  • Assembled contigs
  • Bin0 unassembled reads and Repeat reads

Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query.

Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).
Other Name(s): Tribolium
Parent Organization: Baylor College of Medicine; Texas; USA
Resource Type(s): database, topical portal
Resource: Resource
URL: http://www.hgsc.bcm.tmc.edu/project-species-i-Tribolium%20castaneum.hgsc?pageLocation=Tribolium%20castaneum
*Id: nif-0000-25607
Keywords: genetic, chromosome, coleoptera, drosophila, genome, model, pest, red flour beetle, sequence, tribolium castaneum
Link to OWL / RDF: Download this content as OWL/RDF

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Facts about Resource:Tribolium castaneum Genome ProjectRDF feed
CurationStatuscurated  +
DefiningCitationhttp://www.hgsc.bcm.tmc.edu/project-species-i-Tribolium%20castaneum.hgsc?pageLocation=Tribolium%20castaneum  +
Definition

This portal provides information a
This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below.
The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University).
Access to the Data

- Genome Assembly:

The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder.
A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page.
The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change.

- BLAST Searches:

The BLAST link is located in the sidebar.

  • Linearized chromosome and unplaced scaffold sequences
  • Assembled contigs
  • Bin0 unassembled reads and Repeat reads

Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query.

Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).
DA ARS Agreement No. 58-5430-3-338).
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, and Topical portal  +
Idnif-0000-25607  +
Is part ofBaylor College of Medicine; Texas; USA  +
KeywordsGenetic  +, Chromosome  +, Coleoptera  +, Drosophila  +, Genome  +, Model  +, Pest  +, Red flour beetle  +, Sequence  +, and Tribolium castaneum  +
LabelResource:Tribolium castaneum Genome Project  +
ModifiedDate18 May 2011  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymTribolium  +