scholarly journals Parallel RNA sequence-structure alignment

2004 ◽  
Author(s):  
Tong Liu ◽  
B. Schmidt
Keyword(s):  
Structure Alignment ◽  
Sequence Structure ◽  
Rna Sequence

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 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.

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
Sign in / Sign up

Export Citation Format

Share Document