| Summary: | Summary:Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary
conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the
consideration of all this information together with a recursive permutation-based approach to progressively identify and list the
most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of
complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings.
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