RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments

  • Jakob Hull Havgaard
  • Jan Gorodkin
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)


Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as “RNA structural alignment.” A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns two or more sequences. The advantage of this algorithm over those that separate the folding and alignment steps is that it makes better predictions. The disadvantage is that it is slower and requires more computer memory to run. The amount of computational resources needed to run the Sankoff algorithm is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter.

Key words

Structural RNA alignment Simultaneous folding and alignment of RNA sequences Sankoff algorithm 



This work is supported by the Danish Council for Independent Research (Technology and Production Sciences), the Danish Council for Strategic Research (Programme Commission on Strategic Growth Technologies), as well as the Danish Center for Scientific Computing.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jakob Hull Havgaard
    • 1
  • Jan Gorodkin
    • 1
  1. 1.Center for non-coding RNA in Technology and Health, IKVHUniversity of CopenhagenFrederiksberg CDenmark

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