Titlebook: RNA Structure Prediction; Risa Karakida Kawaguchi,Junichi Iwakiri Book 2023 Springer Science+Business Media, LLC, part of Springer Nature

命令變成大炮

羅盤

Evolutionary Conservation of RNA Secondary Structure,etect positive selection, one should find species-specific structures within a conserved set. This chapter provides protocols to detect and analyze positive selection in ncRNA structures with the SSS-test and other free software.

附錄

CORE

Habituate

ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Need software package, called ResidualBind, that analyzes RNA-protein interactions using only RNA sequence as an input feature and performs global importance analysis for model interpretability. We discuss practical considerations for model interpretability to uncover learned sequence motifs and their secondary structure preferences.

分開(kāi)如此和諧

CAJ

Linear-Time Algorithms for RNA Structure Prediction,Partition lead to more accurate predictions on the longest sequence families for which the structures are well established (16S and 23S Ribosomal RNAs), as well as improved accuracies for long-range base pairs (500?+? nucleotides apart). This chapter provides protocols for using LinearFold and LinearPartition for secondary structure prediction.

chastise

Genome-Wide RNA Secondary Structure Prediction,bles, ParasoR can locally compute the structure scores such as stem probability or accessibility on demand. A comprehensive analysis of local secondary structures by ParasoR is expected to be a promising way to detect the statistical constraints on long RNAs.

和平

憎惡

Web Services for RNA-RNA Interaction Prediction,on tools for specific RNA classes, and RNA-RNA interaction-based RNA design tools. Additionally, we discuss the future perspectives of the development of RNA-RNA interaction prediction tools and the sustainability of web services.