Hi guys,
My question is regarding the pipeline for identification of phasiRNAs in plants.
There are many papers that have used an analysis method but were not very informative on how to execute the protocol.
Links to papers:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457045/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867363/
http://link.springer.com/article/10.1007/s12042-016-9173-4
Method:
The PHAS loci and phasiRNAs were predicted as described previously (Zheng et al. 2014; Srivastava et al. 2015). The unique sequences in the small RNA libraries were mapped to the genome of pineapple with SOAP2 (Li et al. 2009). A self-developed program was used to scan the genome and cDNA sequences using a window of 210 nt or 240 nt (ten 21 nt or 24 nt) respectively. A two-nucleotide positive offset was used to calculate the positions of siRNAs on the anti-sense strand because the existence of two-nucleotide over-hang at the 3’-end of siRNA duplex (Howell et al. 2007; Xia et al. 2013; Chen et al. 2007; Zhai et al. 2011). Then a P-value was calculated for each of the windows using a modified version of methods in Chen et al. (2007),
I would like to know which program can be used to scan the genome with a specific window length as described (Bold) above.
I'd greatly appreciate inputs from anyone who has previous experience in small RNA and specifically phasiRNA analysis.
Thanks
V
I would start with the following tool
GenoScan: Genomic scanner for putative miRNA precursors
we've used the method described here:
Chen, Ho-ming, Yi-hang Li, and Shu-hsing Wu. 2007. “Bioinformatic Prediction and Experimental Validation of a microRNA-Directed Tandem Trans-Acting siRNA Cascade in Arabidopsis.”
look for the Perl script under SI: http://www.pnas.org/content/104/9/3318/suppl/DC1
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