Reducing folding scenario candidates in pseudoknots detection using PLMM_DPSS algorithm integrated with energy filters

Xiaolu Huang, Hesham Ali

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Pseudoknots are important functional structures in RNA. Despite of numerous pseudoknot prediction tools, biologists still need a pseudoknot detection method with much higher sensitivity. We have previously developed the Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking (PLMM_DPSS) algorithm which predicts short loop 2 pseudoknots with high sensitivity. Integrated with Mfold, PLMM_DPSS is capable of predicting both H-type and complicated type pseudoknots. In this study, we have developed PLMM_DPSS_SF_Mfold_FF with the following modifications: the extension of the PLM model to include long loop 2 pseudoknots, the incorporation of overall folding energy calculation, recombination of non-overlapping pseudoknots within one sequence and two filters for higher specificity, The prediction results have shown that PLMM_DPSS_SF_Mfold_FF is more sensitive than other leading pseudoknot prediction tools and results in a low alternative folding number, and results also support the notion that some kinetic barriers may trap RNA folding in local minimums.

Original languageEnglish (US)
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages1299-1303
Number of pages5
DOIs
StatePublished - 2007
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: Jan 14 2007Jan 17 2007

Publication series

NameProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Conference

Conference7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period1/14/071/17/07

Keywords

  • Filter
  • PLMM_DPSS algorithm
  • Pseudoknot prediction

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

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  • Cite this

    Huang, X., & Ali, H. (2007). Reducing folding scenario candidates in pseudoknots detection using PLMM_DPSS algorithm integrated with energy filters. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE (pp. 1299-1303). [4375735] (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE). https://doi.org/10.1109/BIBE.2007.4375735