5838 個技能
Use when aligning long RNA-seq reads to a reference genome using STARlong with SSE3 optimization, or when generating genome indices for long-read splice-aware alignment.
Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.
Use when predicting RNA secondary structures, calculating minimum free energy (MFE) folds, or computing partition functions and base pairing probabilities for RNA sequences.
Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.
Use when predicting locally stable secondary structures from multiple sequence alignments of RNA
Use when searching for RNA sequences that fold into a predefined secondary structure, inverting RNA folding predictions to find sequences matching target bracket notation structures.
Use when analyzing RNA secondary structure landscapes to find local minima via gradient walks, generate barrier trees, or compute rates for kinetic modeling with treekin.
Use when running iterative sequence-to-sequence HMMER searches to expand a protein family from one or a few seed sequences against a sequence database.
Use when converting legacy ViennaRNA 1.8.4 energy parameter files to the 2.0+ format used by modern ViennaRNA tools.
Use when searching an RNA sequence for pseudoknot-forming interactions by combining local accessibility with interaction energy, especially when ordinary pseudoknot-free folding is insufficient.
Use when calculating structure distances between thermodynamic ensembles of RNA secondary structures from sequence input.
Use when aligning long RNA-seq reads (PacBio, Nanopore) to a reference genome using splice-aware mapping with STARlong.
Use when screening a small query RNA against longer target RNA sequences for inter-molecular hybridization sites, especially when optional RNAplfold accessibility profiles should influence the ranking.
Use when computing local RNA secondary structure pair probabilities, scanning large genomes for short stable RNA structures, or analyzing unpaired region probabilities across sliding windows.
Use when working with RNA soft constraints and need to compute pairing probabilities with position-specific perturbation minimization from the ViennaRNA package.
Use when searching target RNAs for interactions with a query H/ACA snoRNA, especially when the search should respect H/ACA-specific structural constraints and optionally use accessibility profiles.
Use when building or reviewing an end-to-end RNA-seq workflow from raw reads through quantification, differential expression, and basic interpretation.
Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.