Variations on RNA folding and alignment: lessons from Benasque.
Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.
Bompfünewerer
Athanasius F
AF
Zentralfriedhof Wien, 3. Tor Simmeringer Haupstrasse, Wien, Austria.
Backofen
Rolf
R
Bernhart
Stephan H
SH
Hertel
Jana
J
Hofacker
Ivo L
IL
Stadler
Peter F
PF
Will
Sebastian
S
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment
D022661:RNA, Untranslated