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The Art of Editing RNA Structural Alignments

  • Ebbe Sloth Andersen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)

Abstract

Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is rewarded by great insight into the evolution of structure and function of your favorite RNA molecule. In this chapter I will review the methods and considerations that go into constructing RNA structural alignments at the secondary and tertiary structure level; introduce software, databases, and algorithms that have proven useful in semiautomating the work process; and suggest future directions towards full automatization.

Key words

RNA structural alignment Comparative analysis Secondary structure Tertiary structure Software Databases Algorithms 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Ebbe Sloth Andersen
    • 1
    • 2
  1. 1.Department of Molecular BiologyAarhus UniversityAarhusDenmark
  2. 2.Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark

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