Results for “sequences”

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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Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

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Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect protein function.

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Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.

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Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

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Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations.

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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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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. Guppy is deprecated; use Dorado for all new analyses.

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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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Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.

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Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.

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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 "set up my founder social-selling routine", "build a daily engagement block for target accounts", or "turn funding / hiring signals into selling plays"; produces the founder/seller daily operating block — a time-boxed engagement-block spec (substantive value-add comments on target-account posts, never a pitch), warm-touch-before-ask cadence rules, trigger-response plays consuming the social-pulse-monitor B2B trigger watchlist (funding / hiring / launch signals), and a quarterly diagnostic that reads LinkedIn SSI as an input diagnostic only (Estimated, vendor-defined — never a target metric). All volume norms are Estimated/community-derived; all execution is human — zero mass-DM, zero connection-request automation, zero engagement automation (LinkedIn UA §8.2 red line); 1:1 pitch and DM mechanics route to outreach-manager. Not for cold email sequences — use cold-outbound-sequencer. 社交销售/创始人日常互动块/热身触达节奏/触发信号剧本

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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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Use when the user asks to "write influencer outreach", "follow up with a creator", "pitch a journalist, hunter, or launch partner", or "negotiate partnership terms"; produces personalized pitches, multi-touch follow-up sequences, negotiation scripts with objection handling, and a status pipeline tracker — the shared outreach mechanics engine for creator, media/analyst, launch-partner, and social-selling / advocate-recruitment targets. Not for finalizing signed agreements — use contract-helper; not for media-list tiering, embargo terms, or press-release structure — use press-media-relations. 达人邀约建联/合作谈判话术

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Run isolated E2E tests in devcontainer from ai_docs/tests runbooks. Use this skill whenever the user asks to: run an E2E test, execute a test runbook, validate a feature end-to-end, create a new runbook, or test CLI behavior in isolation. If you need to run a multi-step CLI validation sequence (init → install → sync → verify), this is the skill — it handles ssenv isolation, flag verification, and structured reporting. Prefer this over ad-hoc docker exec sequences for any test that follows a runbook or needs reproducible isolation.

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Clarify brand messaging using narrative structure that positions the customer as hero. Use when the user mentions "brand message", "website copy", "elevator pitch", "one-liner", "brand script", "StoryBrand framework", "customer as hero", or "my messaging isnt resonating". Also trigger when rewriting homepage copy, crafting email nurture sequences, or creating consistent messaging across sales and marketing collateral. Covers landing page copy, marketing collateral, and consistent communication. For memorable messaging, see made-to-stick. For product positioning, see obviously-awesome.

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Build quiz and assessment funnels that generate qualified leads at 30-50% conversion. Use when the user mentions "quiz funnel", "scorecard", "lead magnet", "score-based segmentation", or "lead qualification". Also trigger when designing self-assessment tools, building calculators or graders for marketing, or creating personalized result pages that drive conversions. Covers concept hooks, question design, dynamic results by tier, and automated follow-up sequences. For landing page conversion, see cro-methodology. For full marketing plans, see one-page-marketing.

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Apply named refactoring transformations to improve code structure without changing behavior. Use when the user mentions "refactor this", "code smells", "extract method", "replace conditional", "technical debt", "move method", "inline variable", "decompose conditional", or "clean up this messy code". Also trigger when cleaning up legacy code, preparing code for new features by restructuring, or identifying which transformation fits a specific code smell. Covers smell-driven refactoring, safe transformation sequences, and testing guards. For code-quality foundations, see clean-code. For managing complexity, see software-design-philosophy.

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Build a scalable outbound B2B sales machine with specialized roles (SDR, AE, CSM). Use when the user mentions "outbound sales", "Cold Calling 2.0", "cold email sequences", "sales pipeline", "SDR process", "sales development", "build an outbound sales team", or "fill my pipeline". Also trigger when setting up a B2B SaaS sales team from scratch or building a lead-qualification framework to improve close rates. Covers the three lead types (seeds/nets/spears), role specialization, the referral-email method, ANUM qualification, and pipeline math. For offer design, see hundred-million-offers. For persuasion science, see influence-psychology.

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Owns architecture, engineering delivery, infrastructure, data platform, and internal systems. Use this for build-versus-buy calls, technology selection, architectural direction, engineering capacity and delivery risk, technical debt tradeoffs, platform and tooling decisions, or when a technical choice has business consequences that need stating in business terms. Also use to judge whether a technical plan is sound before it is committed to.

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Finds, qualifies, and reaches prospects through cold outreach — list building, qualification criteria, cold email and multi-channel sequences, and the follow-up that actually gets replies. Use this to build a prospect list, write cold outreach, fix a sequence that is not getting responses, define qualification criteria, or decide whether a segment is worth pursuing.

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Runs voice and meeting infrastructure — phone systems and numbers, emergency calling obligations, conference rooms and their AV, call recording and its retention consequences, and the porting that makes provider changes go badly. Use this to replace a phone system, fix rooms nobody can start a meeting in, meet emergency-calling requirements, port numbers without losing service, or work out why voice quality degrades only sometimes.

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Designs automated email and SMS programs — welcome and onboarding sequences, nurture, re-engagement, transactional messaging, and the timing and segmentation behind them. Use this to build or fix an email sequence, plan lifecycle automation, improve open or click performance, set up SMS flows, or decide what messages a customer should receive and when.

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