「sequence analysis」の検索結果

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

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Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis.

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Generate Excalidraw diagrams from natural language descriptions. Outputs .excalidraw JSON files openable in Excalidraw. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", "generate an Excalidraw file", "draw an ER diagram", "create a sequence diagram", or "make a class diagram". Supports flowcharts, relationship diagrams, mind maps, architecture, DFD, swimlane, class, sequence, and ER diagrams. Can use icon libraries (AWS, GCP, etc.) when set up. Do NOT use for code architecture analysis (use the architecture skills), Mermaid diagram rendering (use mermaid-studio), or non-visual documentation (use docs-writer).

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Expert Mermaid diagram creation, validation, and rendering with dual-engine output (SVG/PNG/ASCII). Supports all 20+ diagram types including C4 architecture, AWS architecture-beta with service icons, flowcharts, sequence, ERD, state, class, mindmap, timeline, git graph, sankey, and more. Features code-to-diagram analysis, batch rendering, 15+ themes, and syntax validation. Use when users ask to create diagrams, visualize architecture, render mermaid files, generate ASCII diagrams, document system flows, model databases, draw AWS infrastructure, analyze code structure, or anything involving "mermaid", "diagram", "flowchart", "architecture diagram", "sequence diagram", "ERD", "C4", "ASCII diagram". Do NOT use for non-Mermaid image generation, data plotting with chart libraries, or general documentation writing.

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Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

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De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

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Use when the user asks to "build battle cards", "prep the sales team for launch", or "write the internal launch FAQ"; produces the internal enablement kit for a sales-led launch — battle cards vs each named alternative (where we win / where they win / trap questions, every fact traceable), a sales talk track derived from the PR-FAQ spine, an objection-handling table (objection → response → evidence), internal FAQ + CS macros, and an internal launch announcement with embargo discipline. Not for the external message house — use message-house-builder; not for competitor tracking itself — use competitor-tracker or competitor-analysis; not for outbound sequences — use cold-outbound-sequencer. 销售赋能/battle card/销售叙事/异议处理/内部FAQ

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Authoring conventions for exploratory data analysis notebooks and analytical dashboards, covering section sequence, visualization selection, scale thresholds, caching and state, and dashboard validation budgets. Use when composing or reviewing an EDA notebook, an analytical dashboard, or a dashboard test pass.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Design a wise systems intervention from an existing analysis. Maps proposed actions against Meadows' leverage points, checks for unintended consequences, and generates alternatives.

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Accretion/dilution and merger consequences analysis for A-share M&A transactions. Adapted from the original merger-model skill for Chinese GAAP, CAS accounting, and China market transaction structures. Triggers on "A股并购分析", "并购模型", "accretion dilution China", "merger model A-share", or "M&A consequences [company]".

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A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum

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JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis. For ChIP-seq peak motif discovery use homer-motif-analysis; for regulatory variant scoring use regulomedb-database.

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Use Biotite for computational molecular biology workflows: sequence analysis, structure analysis, biological database access, file-format conversion, application wrappers, and optional molecular interfaces.

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Design a wise systems intervention from an existing analysis. Maps proposed actions against Meadows' leverage points, checks for unintended consequences, and generates alternatives.

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Causal reasoning in historical analysis. Covers distinguishing immediate from underlying causes, tracing chains of causation across time scales, identifying unintended consequences, and applying counterfactual reasoning to assess causal significance. Use when analyzing why historical events occurred, evaluating the relative weight of causes, or assessing whether outcomes were inevitable or contingent.

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Stellar spectral analysis from first light to chemical abundance. Covers continuum emission and absorption, the OBAFGKM classification sequence, luminosity classes, line identification, Doppler shifts, curve-of-growth abundance analysis, and the astrophysical conclusions that follow from a spectrum. Use when classifying a star, measuring radial velocity, inferring composition or temperature, or teaching why the Sun is mostly hydrogen.

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Use for architecture review, dependency graphs, coupling analysis, or circular dependency detection. Establishes project module namespaces and traces imports plus Claude plugin hook, skill, script, PEP 723, and MCP boundaries. Emits partitioned Mermaid graphs with cycle, coupling, and ownership signals; verifies contract and consequence before assigning severity. Registers diagrams as codebase-analysis artifacts.

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Specialized prompt-building methodology for content and communications tasks. Provides 11 tested approaches (3 identity, 4 reasoning, 4 output) for writing, editing, content strategy, copywriting, audience analysis, editorial evaluation, cross-channel adaptation, and persuasion design. Use when building a Claude prompt or system prompt for content creation, editorial workflows, or communications tasks. Trigger on: "build a prompt for writing," "prompt for content strategy," "prompt for copywriting," "prompt for blog posts," "prompt for email sequences," "system prompt for editorial," "prompt for messaging framework," "content brief prompt," "prompt for audience analysis," "prompt that produces better content." Do NOT use for writing content directly — this Skill builds prompts that produce better content. Do NOT use for evaluating or scoring existing prompts — use rootnode-prompt-validation if available. Do NOT use for general prompt compilation — use rootnode-prompt-compilation if available.

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Audit and attack session cookies via missing Secure/HttpOnly/SameSite attributes, overly broad Domain/Path scope, non-expiring persistent cookies, absent __Host- and __Secure- prefixes, browser cache leakage (Cache-Control: no-store missing), session token predictability via Burp Sequencer analysis, server-side session not invalidated on logout, and SSO single-logout bypass. Tools: Burp Suite Repeater/Sequencer, OWASP ZAP, EditThisCookie, Tamper Data, Cookiebro.

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Analyzes API call traces from a sandbox or API monitor (JSON) to group calls by category, reconstruct high-level behaviors (process injection, file drops, network, crypto), and flag suspicious call sequences. Activates for requests to analyze an API trace, interpret sandbox API logs, or identify behavior from Win32/Native API calls.

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