TY - JOUR
T1 - Variations on RNA folding and alignment
T2 - Lessons from Benasque
AU - Bompfünewerer, Athanasius F.
AU - Backofen, Rolf
AU - Bernhart, Stephan H.
AU - Hertel, Jana
AU - Hofacker, Ivo L.
AU - Stadler, Peter F.
AU - Will, Sebastian
PY - 2008/1/1
Y1 - 2008/1/1
N2 - 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.
AB - 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.
KW - Dynamic programming
KW - RNA folding
KW - Secondary structure alignment
UR - https://www.scopus.com/pages/publications/36448958364
U2 - 10.1007/s00285-007-0107-5
DO - 10.1007/s00285-007-0107-5
M3 - Article
C2 - 17611759
AN - SCOPUS:36448958364
SN - 0303-6812
VL - 56
SP - 129
EP - 144
JO - Journal of Mathematical Biology
JF - Journal of Mathematical Biology
IS - 1-2
ER -