「fasta」の検索結果

Build robust backend systems with modern technologies (Node.js, Python, Go, Rust), frameworks (NestJS, FastAPI, Django), databases (PostgreSQL, MongoDB, Redis), APIs (REST, GraphQL, gRPC), authentication (OAuth 2.1, JWT), testing strategies, security best practices (OWASP Top 10), performance optimization, scalability patterns (microservices, caching, sharding), DevOps practices (Docker, Kubernetes, CI/CD), and monitoring. Use when designing APIs, implementing authentication, optimizing database queries, setting up CI/CD pipelines, handling security vulnerabilities, building microservices, or developing production-ready backend systems.

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Provides comprehensive code review guidance for React 19, Vue 3, Angular 17+, Svelte 5, Rust, TypeScript, Java, Java 8, PHP, Ruby, Rails, Python, Django, FastAPI, Go, C#/.NET, Kotlin, Swift, Dart, Flutter, NestJS, C/C++, Zig, CSS/Less/Sass, Qt, and more. Covers architecture review, performance review, security audit, code quality anti-patterns, and common bugs across all ecosystems. Use when: reviewing pull requests, conducting PR reviews, code review, reviewing code changes, establishing review standards, mentoring developers, architecture reviews, security audits, performance reviews, checking code quality, finding bugs, giving feedback on code.

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Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.

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Use BEFORE reading any data file that could be large (CSV/TSV, Parquet, HDF5, FITS, NetCDF, NDJSON, genomics FASTQ/FASTA/VCF/BAM, GRIB, ROOT, or big text/simulation logs like VASP OUTCAR). Returns a compact memory pointer — header/schema/shape/sample/key numbers — by introspection and sampling in bounded memory, so you never load a file bigger than the context window into the model. Reference data via the pointer; read specific ranges deterministically.

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You are a Python project architecture expert specializing in scaffolding production-ready Python applications. Generate complete project structures with modern tooling (uv, FastAPI, Django), type hint

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Master Python 3.12+ with modern features, async programming, performance optimization, and production-ready practices. Expert in the latest Python ecosystem including uv, ruff, pydantic, and FastAPI. Use PROACTIVELY for Python development, optimization, or advanced Python patterns.

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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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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Build and deploy AI agents with CloudBase Agent SDK (TypeScript & Python). Implements the AG-UI protocol for streaming agent-UI communication. Use when deploying agent servers, using LangGraph/LangChain/CrewAI adapters, building custom adapters, understanding AG-UI protocol events, or building web/mini-program UI clients. Supports both TypeScript (@cloudbase/agent-server) and Python (cloudbase-agent-server via FastAPI).

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Dub a video into another language and generate subtitles using the default Together + Cartesia stack. Trigger when the user wants to translate / dub / voice-over a video file, or generate subtitles for it. Handles `.mp4` / `.mkv` / `.webm`. Installs as the `violin` CLI (and `violin-api` for the FastAPI server) via `uv tool install`. For alternative models (OpenAI / ElevenLabs) or custom configs, point the user to the repo: https://github.com/shang-zhu/violin.

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Python 开发规范。当用户操作 .py、pyproject.toml、requirements.txt、setup.py 文件， 或涉及 FastAPI、Django、Flask、pytest、asyncio 开发时触发。 包含 PEP 8 风格、类型注解、异常处理、测试规范、异步编程、性能优化等。

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Fullstack development toolkit with project scaffolding for Next.js/FastAPI/MERN/Django stacks and code quality analysis. Use when scaffolding new projects, analyzing codebase quality, or implementing fullstack architecture patterns.

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Server-specific best practices for FastAPI, Celery, and Pydantic. Extends python-skills with framework-specific patterns.

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Universal Runtime best practices for PyTorch inference, Transformers models, and FastAPI serving. Covers device management, model loading, memory optimization, and performance tuning.

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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

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API design and implementation across REST, GraphQL, gRPC, and tRPC patterns. Use when building backend services, public APIs, or service-to-service communication. Covers REST frameworks (FastAPI, Axum, Gin, Hono), GraphQL libraries (Strawberry, async-graphql, gqlgen, Pothos), gRPC (Tonic, Connect-Go), tRPC for TypeScript, pagination strategies (cursor-based, offset-based), rate limiting, caching, versioning, and OpenAPI documentation generation. Includes frontend integration patterns for forms, tables, dashboards, and ai-chat skills.

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API hardening for Express, FastAPI, and serverless. Use for rate limiting, CORS, input validation, API keys, or OWASP API Top 10.

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Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

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Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.

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Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.

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