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DNABERT — pre-trained BERT model for DNA sequence understanding and classification. Tokenizes DNA using overlapping k-mers (k=3,4,5,6) and provides contextualized embeddings for promoter prediction, s
Use with AI
Install the MCP server or CLI to instantly fetch DNABERT documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/dnabert
Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene
1 shared topic • 2 shared operations
Use when working with iPHoP, the Integrated Phage Host Prediction command-line pipeline for predicting bacterial or archaeal host taxonomy from phage and archaeal virus genomes. Covers `iphop predict`
1 shared topic • 2 shared operations
RNAfold is the primary command-line tool in the ViennaRNA Package for RNA secondary structure prediction via minimum free energy (MFE) and partition function algorithms. Predicts MFE dot-bracket struc
1 shared topic • 2 shared operations
Streamlines acquisition and use of environmental predictor datasets for Species Distribution Modeling (SDM).
1 shared topic • 2 shared operations
Zarr — chunked, compressed N-dimensional arrays for Python with cloud-native storage. Provides hierarchical groups, pluggable compression codecs (Blosc, Zstd, Gzip), sharding for large-scale datasets,
1 shared topic • 1 shared operation