Methods for Resequencing Data
We are interested in developing analysis methods for resequencing technologies suchas the Solexa, 454, and ABI SOLiD platforms. In particular we have a number of collaborations that have generated short-read sequencing data on the Solexa platform, and statistical aspects of this technology are an area of research.
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The Piwi proteins of the Argonaute superfamily are required for normal germline development in Drosophila, zebrafish, and mice and associate with 24-30 nucleotide RNAs termed piRNAs. In collaboration with the Miska lab we identified a class of 21-nucleotide RNAs, previously named 21U-RNAs, as the piRNAs of C. elegans. The data were generated from 5'-dependent libraries for wildtype, piwi, mut-7, and dcr-1 mutants and additional 5'-independent libraries for wildtype and piwi mutants that were sequenced using the Illumina/Solexa platform.
In other work we have shown how data produced from these platforms can be used to estimate evolutionary parameters (such as mutation and recombination rates), despite the fact that the data do not necessarily provide complete or aligned sequence information.
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| Selected publications of ours in this area |
- Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavaré S, and Miska E A Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3
transposon mobility in the Caenorhabditis elegans germline. Mol Cell 2008 31, 79-90.
- Jiang R, Tavaré S, and Marjoram P Population genetic inference from resequencing data. Genetics 181, 000-000, in press
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