Parse and convert FASTA, GenBank, FASTQ, and PDB files using Biopython modules.
npx skills add https://github.com/shushuzn/Rairos --skill biopython-shushuzn
Please help me install this Agent Skill. Skill: biopython Source: https://github.com/shushuzn/Rairos/tree/main/skills/biopython Command: npx skills add https://github.com/shushuzn/Rairos --skill biopython-shushuzn
Biopython removes the burden of writing from-scratch parsers and data-access code for common bioinformatics workflows, so you can focus on analysis instead of plumbing.
Use cases: batch-processing sequence files, converting GenBank to FASTA, running BLAST and filtering hits by E-value, computing alignment identities, and extracting/working with protein structure features from PDB data.
Ask the assistant to convert your GenBank file to FASTA and print the sequence lengths for each record.
High-intent search queries and answers about installing and using this skill.
Sequence parsing and format conversion for FASTA, GenBank, and FASTQ is done using Biopython modules like Bio.SeqIO, which extract biological records and convert them into target formats.
Running BLAST searches and filtering results is achieved through the Bio.Blast API, which executes queries and parses XML output to filter hits by metrics like E-value for downstream analysis.
Querying NCBI Entrez databases is supported via the Bio.Entrez API, which requires setting a valid email address to comply with NCBI usage guidelines for programmatic database access.
Computing pairwise and multiple sequence alignments is performed using Biopython's Bio.AlignIO and alignment modules, applying substitution matrices to calculate identities and structural relationships.
Extracting protein structure features from PDB and mmCIF files is handled by the Bio.PDB module, which parses structural data to access atomic coordinates and macromolecular features.
Handling large genomic files is supported by using iterators within Biopython modules, allowing sequential processing of massive datasets without loading entire files into memory.
ovachieverAutomate biological sequence analysis with Biopython for FASTA, GenBank, and BLAST workflows.
galeepConstruct phylogenetic trees from biological sequences using MAFFT, IQ-TREE 2, and FastTree.
jackspaceAnalyze biological sequences for microbiome and ecological data interpretation.
jackspaceParse and write FASTA, GenBank, FASTQ, and PDB files with Biopython.
