Name
Abstract | ||
|---|---|---|
A k-point mutant of a given RNA sequence s = s(1), ..., s(n) is an RNA sequence s' = s'(1),..., s'(n) obtained by mutating exactly k-positions in s; i.e. Hamming distance between s and s' equals k. To understand the effect of pointwise mutation in RNA, we consider the distribution of energies of all secondary structures of k-point mutants of a given RNA sequence.Here we describe a novel algorithm to compute the mean and standard deviation of energies of all secondary structures of k-point mutants of a given RNA sequence. We then focus on the tail of the energy distribution and compute, using the algorithm AMSAG, the k-superoptimal structure; i.e. the secondary structure of a < or =k-point mutant having least free energy over all secondary structures of all k'-point mutants of a given RNA sequence, for k' < or = k. Evidence is presented that the k-superoptimal secondary structure is often closer, as measured by base pair distance and two additional distance measures, to the secondary structure derived by comparative sequence analysis than that derived by the Zuker minimum free energy structure of the original (wild type or unmutated) RNA. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1093/bioinformatics/bti669 | Bioinformatics |
Keywords | Field | DocType |
additional distance measure,k-superoptimal secondary structure,base pair distance,k-point mutant,hamming distance,comparative sequence analysis,rna,pointwise mutations,partition function.,rna sequence,rna molecule,secondary structure,energy landscape,zuker minimum free energy,k-superoptimal structure,base pair,partition function,wild type,rna secondary structure,free energy,standard deviation,fuzzy | Prime (order theory),RNA,Combinatorics,Hamming distance,Bioinformatics,Energy landscape,Protein secondary structure,Base pair,Mathematics,Pointwise,Sequence analysis | Journal |
Volume | Issue | ISSN |
21 | 22 | 1367-4803 |
Citations | PageRank | References |
8 | 0.62 | 8 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| P. Clote | 1 | 84 | 11.55 |
| Jérôme Waldispühl | 2 | 111 | 16.24 |
| Behshad Behzadi | 3 | 93 | 7.29 |
| Jean-Marc Steyaert | 4 | 211 | 49.38 |