Skillware skills · bio/sequence_ops
Sequence Operations
Deterministic in-silico biological sequence operations engine for DNA, RNA, and protein sequences. Performs sequence typing, strict alphabet validation, Watson-Crick reverse complement, transcription, reading-frame translation, Needleman-Wunsch/Smith-Waterman pairwise alignment, structural variant diffing, 6-frame ORF discovery, k-mer profiling with Shannon entropy, and reproducible seeded generation with Biopython.
Capabilities
- Sequence typing (detect_type) for DNA, RNA, and protein molecules
- Strict alphabet, length, and IUPAC ambiguity code validation
- Watson-Crick reverse complement (revcom) and DNA transcription (transcribe)
- Reading-frame translation (translate) with multi-table NCBI genetic codes
- Needleman-Wunsch global and Smith-Waterman local pairwise alignment via Biopython
- Structural variant diffing (variant_diff) calling mutations against reference templates
- 6-frame Open Reading Frame (find_orfs) boundary scanning and candidate translation
- K-mer frequency profiling with top-N words and Shannon entropy calculations
- Reproducible seeded pseudo-random sequence generation with GC bias
Problems this skill solves
People search for tasks — not always "skillware":
- dna reverse complement python agent
- in silico sequence operations ai agent
- translate dna to protein reading frames python
- pairwise sequence alignment needleman wunsch agent
- smith waterman local alignment python agent
- bioinformatics tool for ai agents
- validate iupac dna rna sequence python
- open reading frame orf 6-frame finder python
- k-mer frequency shannon entropy sequence python
- computational biology biopython agent skills
Install
pip install skillware then SkillLoader.load_skill("bio/sequence_ops")
FAQ
- How do I run deterministic biological sequence operations with an AI agent?
- Use Skillware bio/sequence_ops — pip install "skillware[bio_sequence_ops]", load the skill, and pass structured actions: detect_type, validate, revcom, transcribe, translate, pairwise_align, variant_diff, find_orfs, or kmer_profile.
- Does bio/sequence_ops make cloud API calls?
- No. It executes 100% locally and offline in memory using Biopython and bundled knowledge bases in kb/ (codon tables, genetic codes, IUPAC codes, amino acid tables).
- Which genetic codes and alignment modes are supported?
- It supports NCBI Tables 1 (Standard), 2 (Vertebrate Mitochondrial), and 11 (Bacterial/Plastid), and both Needleman-Wunsch global and Smith-Waterman local pairwise alignments.