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Open Access Research article

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

James K Hane13 and Richard P Oliver2*

Author Affiliations

1 Faculty of Health Sciences, Murdoch University, Perth, Western Australia, 6150, Australia

2 Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia

3 Current address: CSIRO Plant Industry, CELS Floreat, Perth, Western Australia, 6014, Australia

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BMC Genomics 2010, 11:655  doi:10.1186/1471-2164-11-655

Published: 24 November 2010

Additional files

Additional file 1:

Test for viable copies of the transposons Molly, Pixie and Elsa in the S. nodorum SN15 genome.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Summary of deRIP improvement and hit discovery scores. Contains summaries of the RIPCAL analyses for highest G:C content, majority consensus and deRIP consensus comparisons. Also contains details of majority and deRIP consensus hits by blastx to the NCBI NR Protein database and by tblastx to the GIRI Repbase database.

Format: XLS Size: 2.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Merging of the previously identified repeat families X3 and R8 to form the new repeat family X3X3R8.

Format: XLS Size: 71KB Download file

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Open Data

Additional file 4:

Merging of the previously identified repeat families X3 and R8 to form the new repeat family X3X3R8. Supplementary Figure, PNG format. The previously predicted X3 and R8 repeat families (HANE and OLIVER 2008) were found to correspond to genomic regions in a distinctive repeated pattern which spanned 26 kB. This region was classified as a new repeat family, X3X3R8, which supersedes the old repeat families R8 and X3. The MUMMER dot-plot above illustrates how the nucleotide majority consensus sequences of R8 and X3 relate to X3X3R8. The first third of the X3X3R8 majority consensus corresponds to a full length copy of X3. The second third of X3X3R8 is comprised of a second, incomplete copy of X3 which in matching regions is 10-20% divergent from the X3 consensus. The final third corresponds to a complete copy of the R8 repeat, in the reverse orientation with respect to its previously defined sequence.

Format: PNG Size: 8KB Download file

Open Data

Additional file 5:

deRIP RIPCAL analysis of the repetitive DNA of S. nodorum SN15. RIPCAL outputs for highest G:C, consensus and deRIP models versus S. nodorum repeat families, tab-delimited txt and gif formats.

Format: XLS Size: 139KB Download file

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Open Data

Additional file 6:

List of predicted functional RecQ helicases in the S. nodorum genome.

Format: ZIP Size: 7.4MB Download file

Open Data