Author: Sperschneider, Jana; Datta, Amitava
Title: DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model Document date: 2010_1_31
ID: q26f8pv4_45
Snippet: DotKnot uses stack probabilities from the probability dot plot as the basis for finding pseudoknot building blocks. At this stage, only a single sequence is accepted as an input. It is well-known that functional pseudoknots are highly conserved in nature, for example in virus families. The pseudoknot detection framework used in DotKnot allows for incorporation of comparative information using aligned probability dot plots. One can expect that rel.....
Document: DotKnot uses stack probabilities from the probability dot plot as the basis for finding pseudoknot building blocks. At this stage, only a single sequence is accepted as an input. It is well-known that functional pseudoknots are highly conserved in nature, for example in virus families. The pseudoknot detection framework used in DotKnot allows for incorporation of comparative information using aligned probability dot plots. One can expect that reliable alignments will greatly improve confidence in the predicted pseudoknots. Especially for complex pseudoknot foldings such as those found in bacterial tmRNA or in the telomerase RNA component, inclusion of comparative information will be invaluable.
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