「sequence」の検索結果

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

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Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

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Dataset annotation management — COCO labels, sequences, export, and Kaggle upload

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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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Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.

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Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated regions beyond annotated coding sequences or quantifying ORF-level translation.

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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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Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.

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Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.

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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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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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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.

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Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.

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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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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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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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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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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Use when the user asks to "build a media list for my launch", "write a launch press release", or "pitch press under embargo"; produces a three-tier media and analyst list (Tier 1 exclusive candidates, Tier 2 vertical press, Tier 3 communities and newsletters), an embargo pitch timing skeleton keyed to the launch-registry date, a press-release draft in standard structure with no fabricated quotes or numbers, and an analyst briefing outline. Not for press-kit assets — use launch-asset-packager; not for follow-up sequence mechanics — use outreach-manager; not for post-launch news-echo monitoring — use launch-monitor. 媒体名单/禁运期pitch/新闻稿/分析师简报

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Use when the user asks to "write the email", "draft subject lines", or "build email creative"; produces the pre-click unit — subject-line variants + preheader, body copy, one clear CTA, and a plain-text alt — message-matched to the destination page and claims-ledger-aware. Not for pre-scoring or ranking subject-line variants (spam/truncation/render pre-score) — use subject-line-lab; not for scoring the email or computing EQS — use email-quality-auditor; not for the multi-step flow — use email-sequence-designer; not for the A/B test plan — use send-experiment-designer. 邮件文案/主题行/邮件创意

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Use when the user asks to "build a preference center", "set up a frequency opt-down ladder", "give people a step-down instead of unsubscribe", or "design a topic/cadence preference page"; produces a preference-center field spec, a frequency/topic opt-down ladder (down-tier paths that substitute for a hard unsubscribe), a preference-to-suppression mapping, and a SEND N-dimension sub-item note on preference-center / frequency options offered. Not for the lifecycle flow map or cadence governance — use email-sequence-designer; not for the consent/suppression record itself — use consent-registry; not for computing EQS or ruling the N1 unsubscribe veto — use email-quality-auditor. 邮件偏好中心/降频阶梯设计/退订替代降档

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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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