Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability prefilter, against the correct database. Covers why plain BLAST is the wrong tool (it scores per-primer similarity, blind to 3'-terminal anchoring and to whether the two primers form a convergent amplicon in range), why a single 3'-terminal mismatch suppresses amplification while internal mismatches are tolerated, why intron-spanning RT-qPCR is defeated by processed pseudogenes that force a GENOME search not transcriptome-only, how to read a Primer-BLAST report (empty unintended-products means none passed its filter, not none exist), and that in-silico checking reduces but never replaces empirical validation. Use when confirming specificity, screening off-target amplicons, avoiding paralog/pseudogene hits, or checking SNPs under the 3' end. Design is primer-basics; dimers primer-validation; alignment read-alignment.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryContent & writingStars0
About this skill
Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability prefilter, against the correct database. Covers why plain BLAST is the wrong tool (it scores per-primer similarity, blind to 3'-terminal anchoring and to whether the two primers form a convergent amplicon in range), why a single 3'-terminal mismatch suppresses amplification while internal mismatches are tolerated, why intron-spanning RT-qPCR is defeated by processed pseudogenes that force a GENOME search not transcriptome-only, how to read a Primer-BLAST report (empty unintended-products means none passed its filter, not none exist), and that in-silico checking reduces but never replaces empirical validation. Use when confirming specificity, screening off-target amplicons, avoiding paralog/pseudogene hits, or checking SNPs under the 3' end. Design is primer-basics; dimers primer-validation; alignment read-alignment.
Quick start
Copy the install prompt. Use the green button above this README.
Send it to your agent. Paste it into your coding agent’s chat and send.
Review the setup. Your agent checks the skill’s instructions, requirements, and installation scope.
Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability prefilter, against the correct database. Covers why plain BLAST is the wrong tool (it scores per-primer similarity, blind to 3'-terminal anchoring and to whether the two primers form a convergent amplicon in range), why a single 3'-terminal mismatch suppresses amplification while internal mismatches are tolerated, why intron-spanning RT-qPCR is defeated by processed pseudogenes that force a GENOME search not transcriptome-only, how to read a Primer-BLAST report (empty unintended-products means none passed its filter, not none exist), and that in-silico checking reduces but never replaces empirical validation. Use when confirming specificity, screening off-target amplicons, avoiding paralog/pseudogene hits, or checking SNPs under the 3' end. Design is primer-basics; dimers primer-validation; alignment read-alignment.
About this listing
Category
Content & writing
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI