Paper Info
Title
Structural RNA alignment by multi-objective optimization.
Abstract
Motivation: The calculation of reliable alignments for structured RNA is still considered as an open problem. One approach is the incorporation of secondary structure information into the optimization criteria by using a weighted sum of sequence and structure components as an objective function. As it is not clear how to choose the weighting parameters, we use multi-objective optimization to calculate a set of Pareto-optimal RNA sequence-structure alignments. The solutions in this set then represent all possible trade-offs between the different objectives, independent of any previous weighting. Results: We present a practical multi-objective dynamic programming algorithm, which is a new method for the calculation of the set of Pareto-optimal solutions to the pairwise RNA sequence-structure alignment problem. In selected examples, we show the usefulness of this approach, and its advantages over state-of-the-art single-objective algorithms.
Year
DOI
Venue
2013
10.1093/bioinformatics/btt188
BIOINFORMATICS
Field
DocType
Volume
Pairwise comparison,Dynamic programming,Data mining,RNA,Weighting,Open problem,Computer science,Source code,Multi-objective optimization,Software,Bioinformatics
Journal
29
Issue
ISSN
Citations 
13
1367-4803
8
PageRank 
References 
Authors
0.56
12
3
Name
Order
Citations
PageRank
Thomas Schnattinger1663.46
Uwe Schöning2998105.69
Hans A. Kestler346844.88