MicroRNA 的鉴定 （MicroRNA identification）PPT.pptVIP

MicroRNA identification based on sequence andstructure alignment;Outline;Introduction;Motivation ;Experiment;Methods (contd) miRAlign Secondary Structure Prediction Both the candidate sequence and it’s reverse complement are analyzed by RNA fold to predict hairpins. Only hairpins with MFE lower than -20 kcal/mol are retained. Pairwise sequence alignment Sequences from previous step are aligned pairwise to all the ~22 nt known miRNA sequences from the training set Sequence similarity score between the candidate and known mature miRNAs is calculated by CLUSTALW. If the score exceeds a user-defined threshold, then the candidate to known miRNA pairs are kept for further analysis ;Methods (contd) Checking miRNA’s position on stemloop 3 properties for miRNA’s position are considered: Should not locate on terminal loop of hairpin Should locate on the same arm of hairpin Position of potential miRNA on hairpin should not differ too much from it’s known homologues Position difference of miRNA on precursors A and B: ;Methods (contd) RNA secondary structure alignment RNAforester computes pairwise structure alignment and gives similarity score Score is a summation of all base (base pair) match (insertion, deletion). Normalized similarity score of structure C and m is given as: ;Methods (contd) Total similarity score After aligning all potential homologue pairs, a total similarity score (tss) is assigned to each candidate sequence. ;;Results;Graph 1 -;Graph 2 -;Comparison of miRAlign with BLAST -;Comparison of miRAlign with ERPIN -;Other results: miRAlign was applied to A. gambiae and 59 putative miRNAs with tss 35 were detected . This was validated when 38 A. gambiae miRNAs were reported in the MicroRNA registry 6.0 and 37 of them were covered by miRAlign miRAlign was also applied to plant, Zea mays and detected 28 out of 40 known Zea Mays miRNAs.;Conclusion;THANK YOU