Results for “fasta”

Enforce API input/output contracts using OpenAPI specifications and JSON Schema to prevent injection, mass assignment, and data leakage attacks.

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.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Provides an adaptive methodology for adding machine learning models to existing codebases, covering problem framing, data readiness, architectural decoupling, and baseline model integration.

Predicts chromatin state across 919 tracks (histone marks, DNase, TF binding) for DNA sequences via the hosted Genomic Intelligence API, producing a report and JSON results.

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.

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

Protect APIs from abuse and resource exhaustion by implementing rate limiting with token bucket, sliding window, and fixed window algorithms using Redis-backed counters, API gateway plugins, or application middleware.

Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Generates complete AI videos through a 6-stage pipeline (script, character/scene design, storyboard, reference images, video generation, post-production) or one-shot pipelines for short videos, action transfer, and digital human dubbing, all running on local servers.

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filter, index, or compute coverage over BAM/CRAM/VCF files. Part of the AlterLab Academic Skills suite.

Server-Sent Events for real-time server-to-client streaming. Express, Fastify, FastAPI, Spring WebFlux SSE implementations. Event streams, reconnection, and EventSource API. USE WHEN: user mentions "SSE", "Server-Sent Events", "EventSource", "event stream", "text/event-stream", "live feed", "streaming updates" DO NOT USE FOR: bidirectional communication - use `socket-io`; WebRTC - use `webrtc`; LLM streaming - use AI SDK skills

Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.

Starlette 1.0 ASGI framework reference with working code examples for every feature. Use this skill whenever writing Starlette applications, building ASGI middleware, working with FastAPI internals, or writing async Python web services. Also trigger when the user mentions Starlette, ASGI, or needs help with routing, WebSockets, middleware, lifespan handlers, or test clients in the Starlette ecosystem — even if they don't name Starlette explicitly but are clearly working with it (e.g., importing from starlette.*, using TestClient with httpx, or writing ASGI scope/ receive/send functions). Covers the 1.0 API exclusively — all deprecated 0.x patterns have been removed.

Reverse-engineer any codebase into a complete Product Requirements Document (PRD). Analyzes routes, components, state management, API integrations, and user interactions to produce business-readable documentation detailed enough for engineers or AI agents to fully reconstruct every page and endpoint. Works with frontend frameworks (React, Vue, Angular, Svelte, Next.js, Nuxt), backend frameworks (NestJS, Django, Express, FastAPI), and fullstack applications. Trigger when users mention: generate PRD, reverse-engineer requirements, code to documentation, extract product specs from code, document page logic, analyze page fields and interactions, create a functional inventory, write requirements from an existing codebase, document API endpoints, or analyze backend routes.

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.

Make sure to use this skill whenever the user mentions anything related to Danish job searching, job listings, job vacancies, employment opportunities in Denmark, or the Danish government job portal — even if they don't mention jobnet.dk explicitly. Also invoke this skill for questions about specific job titles, occupations, employers, or regions in a Danish employment context. This skill covers the official Danish public job portal operated by STAR (Styrelsen for Arbejdsmarked og Rekruttering). Trigger phrases include: danish jobs, danish job search, jobnet, jobnet.dk, find job denmark, danish employment, job i danmark, job på jobnet, offentlige job, stillinger i det offentlige, public sector jobs denmark, government jobs denmark, STAR jobs, job ledige stillinger, ledig stilling, søg job, job opslag, job vacancy denmark, stillingopslag, jobopslag, sygepleje job, ingeniør job, lærer job, pædagog job, it-job denmark, jobs in copenhagen, jobs in aarhus, jobs in odense, deltidsjob, fuldtidsjob, fastansættelse, t