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

2018 ◽  
Author(s):  
Amir H Bayegan ◽  
Peter Clote
Keyword(s):  
Optimal Algorithm ◽  
Structural Information ◽  
Structural Similarity ◽  
Structure Alignment ◽  
Local Alignment ◽  
Global Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Wide Range ◽  
Run Time

AbstractAlignment 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. A number of successful alignment programs are heuristic versions of Sankoff’s optimal algorithm. Most of them require O(n4) run time. This paper describes C++ software, RNAmountAlign, for RNA sequence/structure alignment that runs in O(n3) time and O(n2) space; 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 and STRAL shows that RNAmountAlign has reasonably good accuracy and much faster run time supporting all alignment types.AvailabilityRNAmountAlign is publicly available at http://bioinformatics.bc.edu/clotelab/RNAmountAlign.

TALI: LOCAL ALIGNMENT OF PROTEIN STRUCTURES USING BACKBONE TORSION ANGLES

2008 ◽  
Vol 06 (01) ◽  
pp. 163-181 ◽  
Author(s):  
XIJIANG MIAO ◽  
PETER J. WADDELL ◽  
HOMAYOUN VALAFAR
Keyword(s):  
Sequence Alignment ◽  
Structural Information ◽  
Protein Structures ◽  
Structural Evolution ◽  
Structural Similarity ◽  
Trna Synthetase ◽  
Structure Alignment ◽  
Structural Motif ◽  
Local Alignment ◽  
Torsion Angles

Torsion angle alignment (TALI) is a novel approach to local structural motif alignment, based on backbone torsion angles (ϕ, ψ) rather than the more traditional atomic distance matrices. Representation of a protein structure in the form of a sequence of torsion angles enables easy integration of sequence and structural information, and adopts mature techniques in sequence alignment to improve performance and alignment quality. We show that TALI is able to match local structural motifs as well as identify global structural similarity. TALI is also compared to other structure alignment methods such as DALI, CE, and SSM, as well as sequence alignment based on PSI-BLAST; TALI is shown to be equally successful as, or more successful than, these other methods when applied to challenging structural alignments. The inference of the evolutionary tree of class II aminoacyl-tRNA synthetase shows the potential for TALI in estimating protein structural evolution and in identifying structural divergence among homologous structures. Availability: .

LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA

2004 ◽  
Vol 02 (04) ◽  
pp. 681-698 ◽  
Author(s):  
ROLF BACKOFEN ◽  
SEBASTIAN WILL
Keyword(s):  
Information Structure ◽  
Structure Alignment ◽  
General Definition ◽  
Local Alignment ◽  
Sequence Information ◽  
Sequence Structure ◽  
Worst Case ◽  
Rna Molecules ◽  
Alignment Algorithms ◽  
Local Sequence

Ribonuclic acid (RNA) enjoys increasing interest in molecular biology; despite this interest fundamental algorithms are lacking, e.g. for identifying local motifs. As proteins, RNA molecules have a distinctive structure. Therefore, in addition to sequence information, structure plays an important part in assessing the similarity of RNAs. Furthermore, common sequence-structure features in two or several RNA molecules are often only spatially local, where possibly large parts of the molecules are dissimilar. Consequently, we address the problem of comparing RNA molecules by computing an optimal local alignment with respect to sequence and structure information. While local alignment is superior to global alignment for identifying local similarities, no general local sequence-structure alignment algorithms are currently known. We suggest a new general definition of locality for sequence-structure alignments that is biologically motivated and efficiently tractable. To show the former, we discuss locality of RNA and prove that the defined locality means connectivity by atomic and non-atomic bonds. To show the latter, we present an efficient algorithm for the newly defined pairwise local sequence-structure alignment (lssa) problem for RNA. For molecules of lengthes n and m, the algorithm has worst-case time complexity of O(n2·m2· max (n,m)) and a space complexity of only O(n·m). An implementation of our algorithm is available at . Its runtime is competitive with global sequence-structure alignment.

Placozoa: at least two

Biologia ◽  
2007 ◽  
Vol 62 (6) ◽  
Author(s):  
Matthias Wolf ◽  
Christian Selig ◽  
Tobias Müller ◽  
Nicole Philippi ◽  
Thomas Dandekar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Structure Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Internal Transcribed Spacer 2 ◽  
Compensatory Base Changes

AbstractIt was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE — a tool for synchronous RNA sequence and secondary structure alignment and editing — in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is “no longer a phylum of one”.

scholarly journals LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

2020 ◽  
Author(s):  
Xiaoli Chen ◽  
Nabila Shahnaz Khan ◽  
Shaojie Zhang
Keyword(s):  
Structural Alignment ◽  
Data Bank ◽  
Local Alignment ◽  
Global Alignment ◽  
Rna Structures ◽  
3D Structures ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Alignment Tool ◽  
Wide Range

Abstract A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

A Polyhedral Approach to RNA Sequence Structure Alignment

1998 ◽  
Vol 5 (3) ◽  
pp. 517-530 ◽  
Author(s):  
HANS-PETER LENHOF ◽  
KNUT REINERT ◽  
MARTIN VINGRON
Keyword(s):  
Structure Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Polyhedral Approach
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