Variations on RNA folding and alignment: lessons from Benasque View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-01

AUTHORS

Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will

ABSTRACT

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. More... »

PAGES

129-144

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00285-007-0107-5

DOI

http://dx.doi.org/10.1007/s00285-007-0107-5

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1045280692

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17611759


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