'alignment' 검색 결과

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Build visual territories (mood boards) for team alignment before production. Groups references into 2-4 named territories, each with palette, texture, typography feel, and 4-6 generated sample tiles, so a team can agree on a direction. Use when the user says "moodboard", "visual territories", "align the team on a look", "reference board", or needs stakeholder sign-off on aesthetic before generating final assets. Part of the Creative Production set.

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Frontend UI design, critique, audit, polish. Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Critically review a resume/CV against ATS (applicant tracking system) parsing rules, recruiter skim patterns, and keyword alignment with a target job description. Use when the user asks to "review my resume/CV", "check my resume against this job ad", "will this pass ATS", or shares a resume file (.docx/.pdf/.md) for feedback. Provides scored, prioritised, critical feedback — not a rewrite.

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Challenge vision alignment, value, cost, risk and operating ownership at material scope or release decisions.

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Use when reviewing a README for accuracy, usability, and alignment with the actual repository. Detects invented content, broken setup steps, and structural issues.

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Use when writing, generating, or improving Pest tests for Laravel — clear intent, good coverage, maintainable structure, and alignment with project testing conventions.

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Review a written plan or design doc through a designer's lens before implementation - seven passes over information architecture, interaction states, emotional arc, AI-slop risk, design-system alignment, responsive and accessibility coverage, and unresolved decisions. Each dimension is rated 0-10 with an explicit statement of what would make it a 10, then the plan is edited to get there. Use when a plan has a UI surface and you want the design gaps closed before code is written. Not for auditing a live site.

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Performs a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the user mentions polish, finishing touches, pre-launch review, something looks off, or wants to go from good to great.

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Improve layout, spacing, and visual rhythm. Fixes monotonous grids, inconsistent spacing, and weak visual hierarchy. Use when the user mentions layout feeling off, spacing issues, visual hierarchy, crowded UI, alignment problems, or wanting better composition.

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Creates internal communications for SMEs including employee newsletters, change announcements, town hall agendas, leadership updates, onboarding communications, and team alignment documents. Use when user asks about internal messaging, employee communications, town halls, leadership updates, culture communications, or team announcements.

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Use when revising or reviewing scientific, technical, or academic manuscripts, proposals, abstracts, reports, or related writing for precision, concision, logical cohesion, citation support, evidence alignment, and objective scholarly tone.

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Finalize documentation changes for production readiness by discovering existing conventions, verifying code-doc alignment, reviewing format/terminology/tone consistency, verifying branch/worktree intent, and structuring clean commits with a post-publish branch/worktree cleanup decision. Counterpart of finalize-and-commit for documentation projects.

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Modelo de moderação especializado 7-8B do Meta para filtragem de entrada/saída de LLM. 6 categorias de segurança - violência/ódio, conteúdo sexual, armas, substâncias, automutilação, planejamento criminal. Precisão de 94-95%. Deploy com vLLM, HuggingFace, Sagemaker. Integra com NeMo Guardrails.

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Ajuste fino de LLMs usando reinforcement learning com TRL - SFT para ajuste de instruções, DPO para alinhamento de preferências, PPO/GRPO para otimização de recompensas e treinamento de modelo de recompensas. Use quando precisar de RLHF, alinhar modelo com preferências ou treinar a partir de feedback humano. Funciona com HuggingFace Transformers.

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Framework de segurança em runtime da NVIDIA para aplicações LLM. Com detecção de jailbreak, validação de entrada/saída, verificação de fatos, detecção de alucinações, filtragem de PII, detecção de toxicidade. Usa DSL Colang 2.0 para rails programáveis. Pronto para produção, executa em GPU T4.

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Método da Anthropic para treinar IA inofensiva através de auto-aprimoramento. Abordagem em duas fases - aprendizado supervisionado com auto-crítica/revisão, depois RLAIF (RL from AI Feedback). Use para alinhamento de segurança, redução de outputs prejudiciais sem rótulos humanos. Alimenta o sistema de segurança do Claude.

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认知-工作对齐检查。验证你的实际工作产出是否可追溯到你的认知体系（L1.5原则 or L1文档），识别「漂浮工作」——有执行但无认知根的任务，输出对齐报告。触发词：「检查工作与认知的对齐」「认知根对齐」「这个工作有没有认知根」「认知体系和工作是否自洽」「认知对齐检查」「第四维健康检查」。

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Design engineering principles for making interfaces feel polished. Use when building UI components, reviewing frontend code, implementing animations, hover states, shadows, borders, typography, micro-interactions, enter/exit animations, or any visual detail work. Triggers on UI polish, design details, "make it feel better", "feels off", stagger animations, border radius, optical alignment, font smoothing, tabular numbers, image outlines, box shadows.

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