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 exten...
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| Published in: | Journal of mathematical biology Vol. 56; no. 1-2; pp. 129 - 144 |
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| Main Authors: | , , , , , , |
| Format: | Journal Article |
| Language: | English |
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Berlin/Heidelberg
Springer-Verlag
01.01.2008
Springer Nature B.V |
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| ISSN: | 0303-6812, 1432-1416 |
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| 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. |
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| AbstractList | Issue Title: RNA: Advances in algorithms and mathematics related to the structural biology of RNA 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. 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. 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.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. |
| Author | Hofacker, Ivo L. Will, Sebastian Stadler, Peter F. Bernhart, Stephan H. Bompfünewerer, Athanasius F. Backofen, Rolf Hertel, Jana |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/17611759$$D View this record in MEDLINE/PubMed |
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| Keywords | RNA folding Secondary structure alignment 90C90 Dynamic programming 90C27 92C40 |
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| SubjectTerms | Algorithms Applications of Mathematics Computational Biology - methods Mathematical and Computational Biology Mathematics Mathematics and Statistics Nucleic Acid Conformation RNA, Untranslated - chemistry RNA, Untranslated - genetics Sequence Alignment |
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| Title | Variations on RNA folding and alignment: lessons from Benasque |
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