A benchmark of multiple sequence alignment programs upon structural RNAs

@article{Gardner2005ABO,
  title={A benchmark of multiple sequence alignment programs upon structural RNAs},
  author={P. Gardner and A. Wilm and S. Washietl},
  journal={Nucleic Acids Research},
  year={2005},
  volume={33},
  pages={2433 - 2439}
}
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to… Expand
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