vimalinx/bio-agent - Page 8

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.

rnaduplex

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

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.

rnafold

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

rnaforester

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

rnaheat

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

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.

rnalalifold

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

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.

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.

rnamultifold

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

rnapaln

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

rnaparconv

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

rnapdist

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

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.

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.

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.

rnaplot

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

rnapvmin

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

rnaseq-pipeline

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

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.

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.

rnaup

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

roh-viz

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

rpsblast

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

rpstblastn

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

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.

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.

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.

sam2vcf-pl

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

samtools-pl

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

samtools

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

scn2xml

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

segmasker

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

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.

seqkit

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

seqtk

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

sequence-analysis

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

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.

shuffle-bed

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