skills/claude-scientific-skills
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Timothy Kassis
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scientific-packages/biopython/SKILL.md
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name: biopython
description: Comprehensive toolkit for computational molecular biology using BioPython. Use this skill when working with biological sequences (DNA, RNA, protein), parsing sequence files (FASTA, GenBank, FASTQ), accessing NCBI databases (Entrez, BLAST), performing sequence alignments, building phylogenetic trees, analyzing protein structures (PDB), or any bioinformatics task requiring BioPython modules.
description: Use BioPython for computational molecular biology and bioinformatics tasks. Essential for: sequence manipulation (DNA/RNA/protein transcription, translation, complement, reverse complement), reading/writing biological file formats (FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, PDB, Clustal, PHYLIP, NEXUS), NCBI database access (Entrez searches, downloads from GenBank/PubMed/Protein databases), BLAST sequence similarity searches and result parsing, pairwise and multiple sequence alignments, phylogenetic tree construction and analysis (UPGMA, Neighbor-Joining), protein structure analysis (PDB parsing, secondary structure, structural alignment), sequence property calculations (GC content, melting temperature, molecular weight, isoelectric point), format conversion between biological file types, restriction enzyme analysis, motif discovery, population genetics calculations, and any task requiring Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.Blast, Bio.Align, Bio.Phylo, Bio.PDB, Bio.SeqUtils, or other BioPython modules.
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# BioPython