From: A method for aligning RNA secondary structures and its application to RNA motif detection
Tool Name | Running Time | Space Requirement | Reference |
---|---|---|---|
Sankoffa | O(N6) | O(N4) | [17] |
FOLDALIGNb | O(N4) | O(N4) | [18] |
RAGAc | O(M2N3) | O(M2N2) | [22] |
rna_alignd | min{O(MN3), O(M3N)} | O(MN2) | [26] |
Dynaligne | O(M3N3) | O(M2N2) | [19] |
stemlocf | O(LM) | N/A | [32] |
Rsearchg | O(M3N) | O(M3) | [31] |
RNAforesterh | O(|F1||F2|deg(F1)deg(F2)(deg(F1) + deg(F2))) | O(|F1||F2|deg(F1)deg(F2)) | [27] |
CARNACi | O(N6), O(N2) | O(N4), O(N2) | [20] |
comRNAj | O(MN) | N/A | [21] |