Results for “ncbi-blast”

55 skills

Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.

30.2k · bundle

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite.

Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.

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lucaspmarie-a11y

Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.

Use when converting compatible BLAST annotation XML/ASN streams into a compact gene-markup-style table for downstream EDirect interval helpers.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

nv-segment-ctmr

Runs NV-Segment-CTMR segmentation on CT or MRI NIfTI volumes and records label-map evidence.

Runs chest X-ray reasoning smoke tests using the NV-Reason-CXR-3B model via local inference or a public Hugging Face Space API.

nv-generate-mr-brain-finetune

Finetunes the NV-Generate-CTMR MR-brain diffusion UNet from user-supplied NIfTI training volumes using a wrapper that stages configs and delegates to upstream scripts.

nv-segment-ct-finetune

Fine-tune NV-Segment-CT VISTA3D on CT NIfTI labels for smoke testing or dataset adaptation, wrapping the upstream MONAI bundle entrypoint.

data-breach-blast-radius

Quantifies the business and regulatory impact of a potential data breach by inventorying sensitive data, tracing data flows, scoring exposure vectors, and estimating regulatory fines using law-sourced figures.

36.2k · bundle

nv-generate-mr-brain

Generates synthetic brain MRI volumes using NVIDIA's NV-Generate-CTMR workflow, with configurable modality and random seed.

nemo-mbridge-multi-node-slurm

Convert single-node PyTorch distributed scripts into multi-node Slurm sbatch jobs and debug common multi-node failures, covering srun-native and torch.distributed approaches, container setup, NCCL timeouts, and interactive allocation.

CNB 技能索引

Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.

johnalbertini14-glitch

Queries Belgian railway (NMBS/SNCB) schedules via the iRail CLI, including departures, connections, train compositions, and service disruptions.

alterlab-gene-db

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

CNB 平台交互命令，支持代码仓库、Issue、PR、CI、制品库读写等操作。

neblio-rest-api-suite

Neblio REST API Suite API skill. Use when working with Neblio REST API Suite for ntp1, ins, testnet. Covers 50 endpoints.

Use when converting NCBI XML sequence records to FASTA format, typically after fetching data with efetch from the Entrez Direct toolkit.

Query Belgian railway (NMBS/SNCB) schedules via the irail CLI.

编写、修改、审查 .cnb.yml 流水线配置，诊断构建失败原因并优化性能。

凌不疑（古装虚构）认知与表达框架（压缩蒸馏）：复仇将军、疯批克制、家族血债触发：星汉灿烂等。虚构；禁止暴力教唆

Use when you need to post unique identifiers or accession numbers to NCBI Entrez databases for subsequent retrieval operations

野比大雄（子供向）认知与表达框架（压缩蒸馏）：废柴主角成长线、善良底、道具依赖喜剧触发：哆啦A梦等。勿逐字抄录版权对白

Use when profiling nucleotide content (AT/GC percentages, base counts) of genomic intervals against a FASTA reference.

李白（古典诗人）认知与表达框架（压缩蒸馏）：豪放与自我投射、酒与月意象、功名张力… 触发：诗仙、将进酒等。非历史定论；不伪造诗句

Manage notes, bookmarks, and notebooks using the nb CLI. Create, list, search, and organize notes across multiple notebooks with Git-backed versioning.

music-ingestion-publisher

Ingests music into a LanceDB via ncmdump-rs and sf-cli, searching and downloading from Netease Cloud Music or Bilibili, decrypting local NCM files, and extracting metadata, lyrics, and cover art.

cnb-plugin-market

搜索 CNB 插件市场并生成流水线配置。

Interact with CNB (Cloud Native Build) platform via OpenAPI. Manage organizations, repositories, issues, PRs, merge requests, pipelines, releases, artifacts, workspaces, members, and more. Use `cnb` CLI for CRUD operations. Trigger when user mentions CNB, 云原生构建, or needs to manage CNB resources like repos, issues, PRs, pipelines, releases, or artifact registries.

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.

Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.

jrennie99-glitch

Use the ClawHub CLI to search, install, update, and publish agent skills from clawhub.com. Use when you need to fetch new skills on the fly, sync installed skills to latest or a specific version, or publish new/updated skill folders with the npm-installed clawhub CLI.

Segments abdominal organs from CT NIfTI volumes using the NV-Segment-CT VISTA3D model, producing label maps and structured evidence JSON.

flowstudio-power-automate-debug

Debug failing Power Automate cloud flows by inspecting action-level inputs and outputs through the FlowStudio MCP server.

36.2k · bundle