vimalinx/bio-agent - 第 8 页

rnados

Use when summarizing an RNA folding landscape by counting how many structures fall into each energy band, rather than enumerating individual folds one by one.

原文语言：英语

rnaduplex

Use when computing optimal and suboptimal secondary structures for hybridization of two RNA strands, such as probe-target binding predictions.

原文语言：英语

rnaeval

Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.

原文语言：英语

rnafold

Use when predicting RNA secondary structures, calculating minimum free energy (MFE) folds, or computing partition functions and base pairing probabilities for RNA sequences.

原文语言：英语

rnaforester

Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.

原文语言：英语

rnaheat

Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.

原文语言：英语

rnainverse

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.

原文语言：英语

rnalalifold

Use when predicting locally stable secondary structures from multiple sequence alignments of RNA

原文语言：英语

rnalfold

Use when computing locally stable RNA secondary structures with a maximal base pair span, scanning large genomes for short RNA structures, or predicting local RNA folding with Z-score filtering.

原文语言：英语

rnalocmin

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.

原文语言：英语

rnamultifold

Use when predicting secondary structures and base pairing probabilities for multiple interacting RNA molecules

原文语言：英语

rnapaln

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

原文语言：英语

rnaparconv

Use when converting legacy ViennaRNA 1.8.4 energy parameter files to the 2.0+ format used by modern ViennaRNA tools.

原文语言：英语

rnapdist

Use when calculating structure distances between thermodynamic ensembles of RNA secondary structures from sequence input.

原文语言：英语

rnapkplex

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.

原文语言：英语

rnaplex

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.

原文语言：英语

rnaplfold

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.

原文语言：英语

rnaplot

Use when visualizing RNA secondary structures from dot-bracket notation or Stockholm alignments, generating structure diagrams, or creating annotated consensus structure plots.

原文语言：英语

rnapvmin

Use when working with RNA soft constraints and need to compute pairing probabilities with position-specific perturbation minimization from the ViennaRNA package.

原文语言：英语

rnaseq-pipeline

Use when building or reviewing an end-to-end RNA-seq workflow from raw reads through quantification, differential expression, and basic interpretation.

原文语言：英语

rnasnoop

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.

原文语言：英语

rnasubopt

Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.

原文语言：英语

rnaup

Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.

原文语言：英语

roh-viz

Use when turning `bcftools roh` output plus a VCF/BCF into an interactive HTML visualization of ROH segments and homozygosity rates.

原文语言：英语

rpsblast

Use when searching protein sequences against conserved domain databases like CDD using reverse position-specific BLAST

原文语言：英语

rpstblastn

Use when searching nucleotide sequences against protein domain profile databases (PSSMs) to detect conserved domains via position-specific scoring.

原文语言：英语

run-ncbi-converter

Use when launching an NCBI converter binary through the `run-ncbi-converter` wrapper that downloads and caches the platform-specific executable on demand.

原文语言：英语

run-roh-pl

Use when batch-running `bcftools roh` across a directory of VCF, VCF.GZ, or BCF files and merging the resulting ROH calls across samples.

原文语言：英语

run-with-lock

Use when wrapping a command in NCBI-style file locking so only one worker for a given lock base runs at a time.

原文语言：英语

sam2vcf-pl

Use when converting old `samtools pileup -c` output into VCF and filtering for SNP-only or indel-only calls.

原文语言：英语

samtools-pl

Use when working with samtools.pl, a Perl CLI utility installed by the bioconda samtools package.

原文语言：英语

samtools

Use when working with SAM, BAM, or CRAM alignment files to sort, index, view, convert, or compute statistics.

原文语言：英语

scn2xml

Use when converting SCN-format records into XML for downstream EDirect or XML-based processing.

原文语言：英语

segmasker

Use when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.

原文语言：英语

seq-cache-populate-pl

Use when populating an htslib/CRAM `REF_CACHE` directory from FASTA input or by scanning a directory tree for FASTA files.

原文语言：英语

seqkit

Use when working with FASTA or FASTQ files for statistics, filtering, transformation, format conversion, searching, or set operations.

原文语言：英语

seqtk

Use when doing lightweight FASTA/FASTQ transformations such as conversion, subsampling, subsequence extraction, trimming, or quick QC with seqtk.

原文语言：英语

sequence-analysis

Use when routing DNA, RNA, or protein sequence tasks to the core sequence-analysis commands that are actually installed in this workspace.

原文语言：英语

shift-bed

Use when you need to shift genomic intervals in BED/GFF/VCF files by a specified number of base pairs, either uniformly or strand-specifically.

原文语言：英语

shuffle-bed

Use when you need to randomly permute feature locations across a genome for statistical testing or generating null distributions.

原文语言：英语