miRNomes of haematopoietic stem cells and dendritic cells identify miR-30b as a regulator of Notch1

Su, Xiaoping; Qian, Cheng; Zhang, Qian; Hou, Jin; Gu, Yan; Han, Yanmei; Chen, Yongjian; Jiang, Minghong; Cao, Xuetao

Small RNA annotation. Small RNA sequences were analysed and annotated. We performed database search to assign each small RNA sequence a unique annotation and classify small RNAs into different categories according to their annotations. Unique small RNA sequences were mapped to reference sequences by SOAP (http://soap.genomics.org.cn). We mapped small RNAs to genomic sequences by blast, blast small RNAs against these known non-coding RNAs such as rRNA, tRNA, snRNA and snoRNA which deposited at Rfam database then annotated these small RNAs as 'rRNA etc.' With the repeat annotations of the reference genome available, by a parallel overlap finding algorithm, small RNAs positioned at repeat loci are identified. Using a parallel overlap finding algorithm, small RNAs derived from gene regions also are separated. Small RNAs perfectly matching miRBase precursor sequence were identified as known miRNA. The remained small RNAs were classified as unannotated.