Additional file 6.

Pipeline for the de novo miRNA detection. Figure S3 presents a diagram of computational steps involved in de novo miRNA detection. All reads from SOLiD sequencing were mapped in colorspace to the sorghum genome using SHRiMP. Perfect matching reads were clustered with Vmatch then filtered against the sorghum repeat sequences and compared with know sorghum miRNAs to classify them. The remaining sequences were taken for de novo miRNA prediction using miRDeep.

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Calviño et al. BMC Genomics 2011 12:356   doi:10.1186/1471-2164-12-356