vimalinx/bio-agent - Página 6

jackhmmer

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.

Idioma del texto original: inglés

join-into-groups-of

Use when batching newline-separated IDs into fixed-size comma-separated groups for EDirect calls or other list-limited APIs.

Idioma del texto original: inglés

json2xml

Use when converting JSON documents into XML for downstream EDirect or XML-based processing.

Idioma del texto original: inglés

jsonl2xml

Use when converting JSON Lines streams into XML fragments for downstream EDirect or XML-based processing.

Idioma del texto original: inglés

just-top-hits

Use when keeping only the first N query groups from a first-column-grouped tabular hit table.

Idioma del texto original: inglés

kinfold

Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.

Idioma del texto original: inglés

kinwalker

Use when simulating RNA folding kinetics during transcription to predict cotranscriptional folding pathways and transient intermediate structures.

Idioma del texto original: inglés

legacy-blast-pl

Use when converting NCBI C toolkit BLAST command lines to NCBI C++ toolkit equivalents.

Idioma del texto original: inglés

links-bed

Use when you need to generate HTML links to UCSC Genome Browser from BED, GFF, or VCF feature files.

Idioma del texto original: inglés

mafft

Use when performing multiple sequence alignment on nucleotide or protein sequences, such as preparing alignments for phylogenetic analysis or comparative genomics.

Idioma del texto original: inglés

makeblastdb

Use when creating BLAST databases from FASTA sequence files for use with blastn, blastp, blastx, or other BLAST search tools.

Idioma del texto original: inglés

makehmmerdb

Use when building HMMER binary-formatted sequence databases from plain sequence files, especially for hmmpgmd-style serving or specialized accelerated workflows.

Idioma del texto original: inglés

makembindex

Use when you need to create a BLAST database index for faster search operations on BLAST databases.

Idioma del texto original: inglés

makeprofiledb

Use when creating PSSM databases for rpsblast, cobalt, or deltablast searches. Formats position-specific scoring matrices into BLAST-compatible profile databases.

Idioma del texto original: inglés

map-bed

Use when you need to apply aggregation functions (sum, mean, count, etc.) to values from overlapping intervals in one file and map them onto intervals from another file.

Idioma del texto original: inglés

maq2sam-long

Use when converting legacy MAQ long-map files into SAM for downstream SAMtools-compatible processing.

Idioma del texto original: inglés

maq2sam-short

Use when converting legacy MAQ short-map files into SAM for downstream SAMtools-compatible processing.

Idioma del texto original: inglés

mask-fasta-from-bed

Use when you need to hard-mask or soft-mask regions in a FASTA file using BED, GFF, or VCF coordinates, such as repetitive elements, blacklist regions, or loci to exclude from sequence analysis.

Idioma del texto original: inglés

md5fa

Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5.

Idioma del texto original: inglés

md5sum-lite

Use when computing plain MD5 digests for files or stdin in lightweight HTSlib-based workflows without GNU md5sum features.

Idioma del texto original: inglés

merge-bed

Use when merging overlapping or book-ended intervals in BED/GFF/VCF files into single intervals.

Idioma del texto original: inglés

multi-bam-cov

Use when you need to count read coverage from multiple BAM files across specific genomic regions defined in a BED, GFF, or VCF file.

Idioma del texto original: inglés

multi-intersect-bed

Use when you need to identify overlapping genomic regions across multiple BED files simultaneously.

Idioma del texto original: inglés

multiqc

Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report

Idioma del texto original: inglés

muscle

Use when performing multiple sequence alignment of FASTA inputs, generating alignment ensembles, or calculating alignment confidence metrics.

Idioma del texto original: inglés

nhance-sh

Use when trying the `nhance.sh` shortcut wrapper around `nquire` for pathway, gene-to-pathway, LitVar, or citation-match lookups against NCBI-related endpoints.

Idioma del texto original: inglés

nhmmer

Use when searching DNA or RNA queries against nucleotide sequence databases with HMMER's nucleotide homology search engine.

Idioma del texto original: inglés

nhmmscan

Use when scanning DNA or RNA sequences against a nucleotide profile HMM database such as Dfam to identify annotated families or repeated elements.

Idioma del texto original: inglés

novo2sam-pl

Use when converting legacy Novoalign text output into SAM, especially for unique alignments and optional paired-end interpretation.

Idioma del texto original: inglés

nquire

Use when making raw HTTP, E-utilities, PubChem, datasets, or FTP requests through the low-level EDirect transport wrapper.

Idioma del texto original: inglés

nuc-bed

Use when profiling nucleotide content (AT/GC percentages, base counts) of genomic intervals against a FASTA reference.

Idioma del texto original: inglés

candidate-plan-generator

Use when generating multiple candidate plans from a normalized request before the user approves execution.

Idioma del texto original: inglés

execution-guard

Use when deciding whether a plan stage should continue automatically, pause for confirmation, or escalate because of risk.

Idioma del texto original: inglés

plan-comparator

Use when comparing candidate plans and explaining trade-offs so the user can select or modify a plan.

Idioma del texto original: inglés

plan-editor

Use when incorporating user changes into a selected plan while preserving execution structure and validation semantics.

Idioma del texto original: inglés

request-normalizer

Use when turning a natural-language biology request into a structured request object before planning.

Idioma del texto original: inglés

run-resumer

Use when resuming a paused or interrupted run from saved run state instead of regenerating the plan from scratch.

Idioma del texto original: inglés

skill-router

Use when expanding an approved plan into stage-by-stage candidate skills drawn from the local skill registry.

Idioma del texto original: inglés

stage-reviewer

Use when checking whether a completed stage produced the artifacts and validation evidence required by the approved plan.

Idioma del texto original: inglés

pair-at-a-time

Use when turning a plain-text stream into adjacent lowercase word pairs for EDirect-style text mining, token-neighbor extraction, or lightweight bigram generation.

Idioma del texto original: inglés