RNA Multiple Sequence Alignments

T-Coffee contains a special mode named "R-Coffee" for aligning non-coding RNAs with conserved secondary structures. In this section we show how this mode can be used and how the resulting alignments can be analyzed for compensated mutations. For this purpose we used an alignment derivedĀ  from DARTS, a database of RNA sequences with known 3D-structure [36].

  1. Aligning RNA Sequences with R-Coffee
  2. Evaluating RNA multiple Sequence Alignments