'sequences' 검색 결과

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

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The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules fr

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ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

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MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.

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syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-bas

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A toolset for deciphering and managing biological sequences.

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doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a s

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Use when the user asks about Vibe Motion, motion graphics, kinetic typography, animated text, brand animations, logo animations, infographic animation, presentation animation, data-driven video, or prompt-to-motion-graphic workflows. Vibe Motion is fundamentally different from video generation — it creates deterministic code-based motion graphics, not AI-predicted pixel sequences. Use this when the text/logo must stay perfectly crisp and editable (code). For a cinematic/kinetic AI-generated video ad built from a storyboard (pixel render, native audio), use higgsfield-motion-design instead.

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Build a WhatsApp marketing strategy — WhatsApp Business setup, broadcast campaigns, automated flows, customer service, drip sequences, and conversational marketing. Use when the user says "WhatsApp marketing", "WhatsApp Business", "WhatsApp campaigns", "WhatsApp broadcasts", "WhatsApp automation", "WhatsApp drip", "market on WhatsApp", "WhatsApp for business", "WhatsApp chatbot", "WhatsApp customer service", "WhatsApp API", "messaging marketing India", or wants to use WhatsApp as a marketing and customer communication channel. Especially relevant for brands in India, the Middle East, Southeast Asia, Brazil, and Africa.

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Improve user onboarding flows to increase activation and retention. Use when asked to design welcome screens, setup wizards, product tours, onboarding checklists, or activation sequences. Trigger phrases: "onboarding flow", "user activation", "welcome screen", "product tour", "onboarding checklist", "first-run experience", "setup wizard", "aha moment", "time to value", "user onboarding", "activation rate".

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Use when the user needs B2B pipeline work — ICP and account lists, prospecting, cold email and LinkedIn outbound sequences, lead scoring, MQL to SQL handoff, sales decks, objection handling, demo scripts, CRM pipeline hygiene, and RevOps reporting. Trigger on 'find leads', 'prospect list', 'cold email sequence', 'outbound campaign', 'lead scoring model', 'our pipeline is empty', 'sales deck for enterprise buyers'. Also use when the user has a strong product and no route to the companies that need it. Not for — consumer lifecycle email, see `14-email-marketing-global`; the offer being sold, see `31-offer-design-global`; positioning against rivals, see `58-positioning-global`; inbound content, see `36-content-brief-global`.

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JTBD workflow classification and routing - ODI two-phase framework, five job types with workflow sequences, baseline type selection, workflow anti-patterns, and common recipes

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Records one architecture decision with alternatives, consequences and status; does not design the whole system.

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A complete marketing department in one skill. Website and landing-page audits with weighted 0-100 scores, copywriting with panel scoring and AI-slop removal, an 18-tactic ad hook engine, GEO/AEO for getting cited by ChatGPT/Perplexity/AI Overviews, paid-ads creative diagnosis and production briefs, email sequences, LinkedIn/X writing, launch playbooks, positioning and offer design, competitor teardowns, app store optimization, honest analytics and test design. Use for ANY marketing task — audit, write, rewrite, diagnose, score, plan, launch, position, price, analyze — whenever the user mentions marketing, growth, conversion, copy, ads, hooks, CPM, ROAS, SEO, GEO, email, social, landing pages, funnels, launches, competitors, brand, positioning, pricing, or app stores, or says "my landing page sucks", "nobody's converting", "why are my CPMs up", "AI doesn't recommend us", "write me 20 hooks". Route via the table inside; fan out subagents for multi-dimensional work. Not for pure engineering, legal, or finance.

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Detect and recover text that was accidentally typed with the Taiwanese Bopomofo / Zhuyin (注音) keyboard while the input method (IME) was stuck in English/ASCII mode — what Taiwanese users call 注音亂碼 or 注音文 — producing meaningless-looking letter+digit sequences such as "su3cl3a8", "cl3", "g4", "2k7", "vu,4", or such garbled runs embedded in an otherwise normal request (e.g. "help me fix su3cl3a8", "看看這個 PR qk4ru.6", "幫我改 su3cl3a8xk7"). Use this skill whenever a user message contains short ASCII tokens that look like keyboard gibberish, do not form real English words, and cannot be understood normally — especially tokens with digits interspersed among letters (tone keys 3/4/6/7 or vowel keys 8/9/0), which are a strong sign of Mandarin phonetic keystrokes typed in the wrong input mode. Run scripts/decode_bopomofo.py to deterministically map the keystrokes back to 注音 symbols with a confidence score, then interpret the intended Traditional Chinese in context and continue the user's original request without making them retype. Do NOT trigger on genuine technical strings — code, file paths, URLs, git hashes, CLI flags, package names, version numbers — the script's exclusion rules and confidence tiers already filter these out. Especially valuable for Taiwanese developers who forget to switch input methods when prompting AI coding agents.

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Generate cinematic AI shortfilm prompts (works with Seedance 2.0, Xiaoyunque, Sora, Kling, Jimeng, Veo) using the 5-stage structure from Mx-Shell's Zombie Scavenger. Trigger when the user wants transformation sequences, multi-shot narrative shorts, weapon-charge/combat segments, emotional family/pet/farewell narratives (催泪/亲情/萌宠/离别), or any cinematic video prompt.

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Build evidence-backed day trips, multi-day itineraries, and efficient stop sequences with Google Maps data through the standalone CLI. Use when the desired output is a practical travel plan, not merely a route or list of places.

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Build personalized cold outreach sequences for LinkedIn and email. Use when someone needs to reach prospects, warm up cold leads, or build a systematic outreach engine. Covers research, connection requests, follow-ups, and conversion.

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Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

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Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

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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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Deliberate-choice procedure for a medium-to-high-stakes engineering fork — when the first plausible solution (the instinct, the default next-token pull) would be costly to get wrong. Fires AUTONOMOUSLY: invoke proactively whenever a fork fits, never wait to be asked — mechanical triggers include a fix failing for the 2nd-3rd time, adding a dependency, schema/migration design, deleting or deprecating things others depend on, changing a public API, choosing an architecture or stack. Refuse the premature collapse: hold real options open (urge · contrarian · synthesis · out-of-box · intuitive dots · precedent · first-principles), ground each branch in at least one fact from outside the model (codebase, docs, benchmark, spike), future-model consequences (blast radius, reversibility, maintenance, pre-mortem), collapse by deliberate choice, then try to refute the winner before acting. Log the decision and rejected branches in docs/decision_logs/. Not for routine calls — a decision worth more than one forward pass.

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