AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-alignment-pairwise
Maintainer FreedomIntelligence · Last updated April 1, 2026
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-pairwise
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: PairwiseAligner() (BioPython Bio.Align).
- CLI: needle (global) or water (local) from EMBOSS.
- R: pairwiseAlignment() (Biostrings).
- Align two sequences" → Compute an optimal alignment between a pair of sequences using dynamic programming. Python: PairwiseAligner() (BioPython Bio.Align) CLI: needle (global) or water (local) from EMBOSS R: pairwiseAlignment() (Biostrings).
- Align two sequences using dynamic programming algorithms (Needleman-Wunsch for global, Smith-Waterman for local).
Source Doc
Excerpt From SKILL.md
Required Import
Goal: Load modules needed for pairwise alignment operations.
Approach: Import the PairwiseAligner class along with sequence and I/O utilities from Biopython.
Core Concepts
| Mode | Algorithm | Use Case |
|---|---|---|
global | Needleman-Wunsch | Full-length alignment, similar-length sequences |
local | Smith-Waterman | Find best matching regions, different-length sequences |
Creating an Aligner
Goal: Configure a PairwiseAligner with appropriate scoring for the sequence type.
Approach: Instantiate PairwiseAligner with mode, scoring parameters, or a substitution matrix depending on DNA vs protein input.
Use cases
- Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- alignment-io - Save alignments to files in various formats
- msa-parsing - Work with multiple sequence alignments
- msa-statistics - Calculate identity, similarity metrics
- sequence-manipulation/motif-search - Pattern matching in sequences
Related skills
Related skills
AL
Data & Repro
alphafold
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) P…
FreedomIntelligence/OpenClaw-Medical-SkillsView
AN
Data & Repro
antibody-design-agent
Antibody design: epitope mapping, CDR engineering, bispecific construction.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bindcraft
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2)…
FreedomIntelligence/OpenClaw-Medical-SkillsView