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Alignment of structural RNAs is an important problem with a wide range ofapplications. Since function is often determined by molecular structure, RNAalignment programs should take into account both sequence and base-pairinginformation for structural homology identi^Lcation. A number of successfulalignment programs are heuristic versions of Sanko^K's optimal algorithm. Mostof them require O(n4) run time. This paper describes C++ software,RNAmountAlign, for RNA sequence/structure alignment that runs in O(n3) time andO(n2) space; moreover, our software returns a p-value (transformable to expectvalue E) based on Karlin-Altschul statistics for local alignment, as well asparameter ^Ltting for local and global alignment. Using incremental mountainheight, a representation of structural information computable in cubic time,RNAmountAlign implements quadratic time pairwise local, global andglobal/semiglobal (query search) alignment using a weighted combination ofsequence and structural similarity. RNAmountAlign is capable of performingprogressive multiple alignment as well. Benchmarking of RNAmountAlign againstLocARNA, LARA, FOLDALIGN, DYNALIGN and STRAL shows that RNAmountAlign hasreasonably good accuracy and much faster run time supporting all alignmenttypes.

RNAmountAlign: efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment