「sequence」の検索結果

Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.

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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Query Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".

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Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.

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Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

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Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Chai-1 structure prediction for protein complexes and design validation. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For ESM-based analysis, use esm2-sequence-scoring.

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Complete marketing pipeline for apps, dev tools, libraries, and SaaS products in 2026. Generates positioning, listing/ASO/package-SEO assets, press kit, launch plan, social calendar, email sequences, growth/referral strategy, paid playbook, retention, and community plan. Adapts automatically to app vs dev-tool vs SaaS. Trigger on: marketing, launch plan, app launch, go-to-market, ASO, press kit, product hunt launch, hacker news launch, dev tool marketing, growth strategy, launch checklist, marketing plan, distribution plan.

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generate, refine, validate, and render diagrams from natural language, notes, code snippets, schemas, tables, or existing diagram source. use for flowcharts, swimlanes, sequence diagrams, state diagrams, er diagrams, class diagrams, architecture/c4-style diagrams, dependency graphs, gantt charts, mind maps, user journeys, sankey-style flows, org charts, network graphs, and other visual models. supports mermaid by default, graphviz dot for complex graph layout, plantuml for uml-heavy engineering diagrams, and svg output when direct markup is more reliable.

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Use when reviewing, auditing, scoring, or improving a real or synthetic MATLAB AI tutor transcript, tutoring prompt, generated lesson, exercise, feedback sequence, or skill behavior for MATLAB accuracy, active learning, assignment guardrails, feedback quality, debugging support, transfer prompts, and instructor-facing quality recommendations.

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Sequenced launcher that bootstraps QA on a project with no QA in place. Chains qa-project-context → test-strategy → test-planning in one guided run, then points you at automation. Use when: "set up QA on a new project," "QA from scratch," "no QA exists yet," "/qa-start." Not for: onboarding a QA engineer to an existing team with existing tests — use qa-project-bootstrap. Not for: "which skill do I use" with no clear match — use qa-do. Related: qa-project-context, test-strategy, test-planning, qa-project-bootstrap, qa-do.

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Allocate launch channels using the Owned / Rented / Borrowed (ORB) framework during PRD v0.9 Go-to-Market. Triggers on requests to pick launch channels, distribute the offer, build a channel portfolio, or when user asks "where do we launch?", "what channels?", "ORB", "owned vs rented vs borrowed", "channel allocation", "channel mix", "Corey Haines launch". Outputs GTM-* entries with Type=Channel, a channel-mix matrix, and a launch sequence.

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Orchestrate go-to-market strategy by running positioning, offer construction, and channel allocation as a sequenced workflow during PRD v0.9 Go-to-Market. Triggers on requests to plan launch, define GTM strategy, or when user asks "how do we launch?", "go-to-market", "launch plan", "marketing strategy", "GTM", "launch this product". Chains three framework-grounded sub-skills (Dunford → Hormozi → ORB) and reconciles their outputs.

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Writes and rewrites the words on marketing pages: homepage, landing page, pricing, feature, product and about pages, including headlines, button text, section copy, title tag and meta description. Starts from the reader's own language and the proof the business can show, edits copy where it lives in the repository, and flags every claim that needs evidence. Use when someone says "write copy for this page", "rewrite our homepage", "this page sounds generic", "headline ideas", "better CTA", "landing page copy for this ad" or "pricing page wording". Email copy belongs to email-sequence, popups to popup-cro, and line-editing a finished draft to copy-editing.

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You are an expert in Clay, the data enrichment and outbound sales platform that pulls from 75+ data providers to build rich prospect profiles. You help teams automate lead discovery, enrich contacts with firmographic and technographic data, score leads against ICP criteria, and trigger personalized outreach sequences — replacing manual research with automated, data-driven prospecting.

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Automate video editing in Blender's Video Sequence Editor with Python. Use when the user wants to add video, image, or audio strips, create transitions, apply effects, build edit timelines, batch assemble footage, estimate render times, or script any VSE workflow from the command line.

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World-class motion graphics expertise combining the animation principles of Disney, the kinetic typography of MK12, and the visual storytelling of studios like Buck and Ordinary Folk. Motion graphics transforms static ideas into dynamic visual experiences. Great motion graphics doesn't just move—it communicates. Every animation should have purpose: to guide attention, reinforce message, create emotion, or clarify concept. The best motion designers understand that restraint is power, that timing is everything, and that the animation should be invisible—viewers should feel the story, not notice the effects. Use when "motion graphics, animation, animate, motion design, kinetic, logo animation, title sequence, lower thirds, animated, after effects, lottie, transitions, motion, motion, graphics, animation, after-effects, lottie, kinetic, typography, design" mentioned.

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Your first 10 hires determine your company culture. Your first 50 determine your execution capacity. Hiring is the most leveraged activity a founder does, and the most common source of expensive mistakes. This skill covers when to hire, who to hire first, how to sequence roles, compensation and equity, interviewing and closing, and the many ways hiring goes wrong at startups. Use when "hiring, first hire, when to hire, who to hire, compensation, equity, salary, recruiting, interview process, offer negotiation, team building, engineer hire, sales hire, founding team, hiring, team, compensation, equity, recruiting, interviews, offers, startups, founding-team" mentioned.

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