bio-primer-design-primer-basics
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers.
npx skills add BioTender-max/awesome-bio-agent-skills --skill primer-basics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, pandas 2.2+, primer3-py 2.0+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # PCR Primer Design **"Design primers for this sequence"** → Given a template sequence and constraints (product size, Tm, GC%), find ranked primer pairs that amplify the target region. - Python: `primer3.design_primers()` (primer3-py) - CLI: `primer3_core` (Primer3) Design PCR primers using primer3-py, the Python binding for Primer3. ## Required Imports ```python import primer3 from primer3 import p3helpers from Bio import SeqIO from Bio.Seq import Seq ``` ## Sequence Preparation (p3helpers) ```python # Sanitize sequence (uppercase, remove whitespace) raw_seq = ' atgc gatc GATC ' clean_seq = p3helpers.sanitize_sequence(raw_seq) print(f'Cleaned: {clean_seq}') # 'ATGCGATCGATC' # Reverse complement for designing reverse primers seq = 'ATGCGATCGATC' rc_seq = p3helpers.re
- Version Compatibility
- Required Imports
- Sequence Preparation (p3helpers)
- Basic Primer Design
- Extract Primer Results
- Target a Specific Region
- Primers Must Span a Region
- Exclude Regions
- Constrain Primer Positions
- Design for Sequencing
- Full Parameter Control
- Load Sequence from FASTA
- Calculate Tm Directly
- Tm Calculation Defaults
What does the bio-primer-design-primer-basics skill do?
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill primer-basics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.