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

Autoři: Amir H. Bayegan aff001;  Peter Clote aff001
Působiště autorů: Biology Department, Boston College, Chestnut Hill, MA, United States of America aff001
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0227177


Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identification. This paper describes C++ software, RNAmountAlign, for RNA sequence/structure alignment that runs in O(n3) time and O(n2) space for two sequences of length n; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics for local alignment, as well as parameter fitting for local and global alignment. Using incremental mountain height, a representation of structural information computable in cubic time, RNAmountAlign implements quadratic time pairwise local, global and global/semiglobal (query search) alignment using a weighted combination of sequence and structural similarity. RNAmountAlign is capable of performing progressive multiple alignment as well. Benchmarking of RNAmountAlign against LocARNA, LARA, FOLDALIGN, DYNALIGN, STRAL, MXSCARNA, and MUSCLE shows that RNAmountAlign has reasonably good accuracy and faster run time supporting all alignment types. Additionally, our extension of RNAmountAlign, called RNAmountAlignScan, which scans a target genome sequence to find hits having high sequence and structural similarity to a given query sequence, outperforms RSEARCH and sequence-only query scans and runs faster than FOLDALIGN query scan.

Klíčová slova:

Multiple alignment calculation – RNA alignment – RNA folding – RNA structure – Sequence alignment – Sequence databases – Transfer RNA – RNA sequences


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