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RNA seq.txt (79, 2009-11-21)
NussinovRNA.py (5034, 2009-11-18)

1.Function: This program implements Nussinov algorithm on predicting RNA structure from RNA sequence using dynamic programming approach. The baisic idea is similiar with Smith-Waterman algorithm, obtaining optimal result about predicting RNA secondary structure. This program is able to deal with "bulge","hairpin loop" efficiently but can not handle "pseudoknot'. The program gives the number of matched base pairs and implement traceback procedure to get every pair of matched ribonucleic acid. 2.Input: There are two parameters for user to define. -s sequence: user defined input sequence file, in **fasta format -n hairpin loop size: which indicates the minimal hairpin loop size. Based on this parameter, the predicted RNA structure will have a hairpin loop which size is no smaller than specified. 3.Output: The default output file name is "RNA structure.out", which contains two results: one is number of match base pairs and another is each pair of match robonucleotides. for example: Number of base pairs of the predicted structure: 5 base-pair # 0: 1(A) - 20(U) base-pair # 1: 3(G) - 19(C) base-pair # 2: 5(C) - 16(G) base-pair # 3: 6(U) - 15(A) base-pair # 4: 7(C) - 14(G) 4.Sample Uasge: Run from command line like:(user has to specify 2 parameters, one is input sequence file name and another is minimal loop size) python NussinovRNA.py -s file -n size

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