vimalinx/bio-agent - Seite 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.

Quellsprache: Englisch

join-into-groups-of

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

Quellsprache: Englisch

json2xml

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

Quellsprache: Englisch

jsonl2xml

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

Quellsprache: Englisch

just-top-hits

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

Quellsprache: Englisch

kinfold

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

Quellsprache: Englisch

kinwalker

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

Quellsprache: Englisch

legacy-blast-pl

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

Quellsprache: Englisch

links-bed

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

Quellsprache: Englisch

mafft

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

Quellsprache: Englisch

makeblastdb

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

Quellsprache: Englisch

makehmmerdb

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

Quellsprache: Englisch

makembindex

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

Quellsprache: Englisch

makeprofiledb

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

maq2sam-long

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

Quellsprache: Englisch

maq2sam-short

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

md5fa

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

Quellsprache: Englisch

md5sum-lite

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

Quellsprache: Englisch

merge-bed

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

multi-intersect-bed

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

Quellsprache: Englisch

multiqc

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

Quellsprache: Englisch

muscle

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

nhmmer

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

Quellsprache: Englisch

nhmmscan

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

Quellsprache: Englisch

novo2sam-pl

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

Quellsprache: Englisch

nquire

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

Quellsprache: Englisch

nuc-bed

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

Quellsprache: Englisch

candidate-plan-generator

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

Quellsprache: Englisch

execution-guard

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

Quellsprache: Englisch

plan-comparator

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

Quellsprache: Englisch

plan-editor

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

Quellsprache: Englisch

request-normalizer

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

Quellsprache: Englisch

run-resumer

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

Quellsprache: Englisch

skill-router

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

Quellsprache: Englisch

stage-reviewer

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

Quellsprache: Englisch

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.

Quellsprache: Englisch