Seq2Bio: A Colab‑based tool for protein‑centric biological context retrieval
Seq2Bio: A Colab‑based tool for protein‑centric biological context retrieval
Seq2Bio is a comprehensive Google Colab notebook that transforms a protein sequence into a rich biological report. It integrates multiple public databases (NCBI BLAST, NCBI Taxonomy, iNaturalist, GBIF, PubMed) and tools (Clustal Omega, AlphaFold DB, ColabFold) to provide: BLAST homology search (≥70% identity) Taxonomic lineage Organism images and common names Interactive geographic map with hover tooltips (species, common name, image, location) Relevant PubMed publications (toxin/venom focused, but customisable) Multiple sequence alignment and phylogenetic tree (Newick format) Protein structure retrieval from AlphaFold DB or prediction via ColabFold, with confidence plots (pLDDT, PAE) and Ramachandran plots Downloadable ZIP archive of all results Email notification upon completion
If you use Seq2Bio in your research, please cite it as below.
phylogenetics, protein sequence, Google Colab, bioinformatics, AlphaFold, BLAST
phylogenetics, protein sequence, Google Colab, bioinformatics, AlphaFold, BLAST
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