Chapter

Structural and Evolutionary Considerations for Multiple Sequence Alignment of Rna, and the Challenges for Algorithms That Ignore Them

Karl M. Kjer, Usman Roshan and Joseph J. Gillespie

in Sequence Alignment

Published by University of California Press

Published in print November 2009 | ISBN: 9780520256972
Published online March 2012 | e-ISBN: 9780520943742 | DOI: http://dx.doi.org/10.1525/california/9780520256972.003.0007
Structural and Evolutionary Considerations for Multiple Sequence Alignment of Rna, and the Challenges for Algorithms That Ignore Them

Show Summary Details

Preview

This chapter discusses the biological motivations for aligning data and explores the limitations of strict algorithmic approaches, focusing on the alignment of structural RNAs, or ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences, for phylogenetic analysis. It emphasizes the importance of including both structural and evolutionary information in post-algorithmic manual curation of alignments. The chapter also suggests that further development of RNA alignment benchmarks, better substitution scoring matrices, and adaptation of techniques used in state-of-the-art protein alignments will lead to better algorithms for aligning RNA.

Keywords: structural RNAs; ribosomal RNA; transfer RNA; RNA alignment; protein alignments

Chapter.  14324 words.  Illustrated.

Subjects: Evolutionary Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.