PrimerJinn
primerJinn has two main functions: it designs primers for multiplex PCR of given target regions in a DNA sequence (FASTA file) and performs in silico PCR given a list of primers and a reference FASTA file.
Features
- Multiplex Primer Design: Design optimal primer sets for multiple target regions
- In Silico PCR: Simulate PCR reactions with your primers against a reference sequence
- Primer Interaction Analysis: Check for primer dimers and cross-reactions
- Q5 Polymerase Support: Optimized settings for NEB Q5 hotstart polymerase
- Illumina Compatibility: Option to add Illumina partial adapters
- Comprehensive Output: Excel workbooks with detailed primer information and interactions
Installation
pip install primerJinn
System Requirements
- Python 3.6+
- BLAST+
Usage
1. Multiplex Primer Design
getMultiPrimerSet \
--region_file "./example/primer_regions.tsv" \
--input_file "./example/ref.fasta" \
--target_tm 65 \
--primer_len 20 \
--product_size_min 400 \
--product_size_max 800 \
--ret 100 \
--Q5 \
--output "example" \
--output_fasta \
--exclude_primers
2. In Silico PCR
PCRinSilico \
--primer_seq ./example/primers.txt \
--target_tm 50 \
--input_file ./example/ref.fasta \
--output "in_silico_PCR" \
--output_fasta \
--exclude_primers
Parameters
Common Parameters (Both Tools)
| Parameter | Required | Description | Default |
|---|---|---|---|
--input_file |
Yes | Reference FASTA file path | NA |
--target_tm |
No | Target melting temperature (°C) | 60 |
--salt_concentration |
No | Salt concentration (nM, ignored if Q5=True) | 50 |
--output |
No | Output file prefix | 'MultiPlexPrimerSet' or 'in_silico_PCR' |
--Q5 |
No | Use Q5 polymerase settings | False |
--output_fasta |
No | Output amplicon sequences in FASTA format | False |
--exclude_primers |
No | Exclude primer sequences from FASTA output | False |
Primer Design Specific Parameters
| Parameter | Required | Description | Default |
|---|---|---|---|
--region_file |
Yes | TSV/XLSX file with regions (name, start, end) | NA |
--primer_len |
No | Primer length | 20 |
--product_size_min |
No | Minimum amplicon size | 400 |
--product_size_max |
No | Maximum amplicon size | 800 |
--ret |
No | Maximum primer pairs to return | 100 |
--background |
No | Mispriming library FASTA | None |
--ill_adapt |
No | Add Illumina partial adapters | False |
--clamp |
No | Require GC clamp | 0 |
--poly |
No | Max mononucleotide repeat length | 3 |
--no_self_background |
No | Skip self-mispriming check | False |
In Silico PCR Specific Parameters
| Parameter | Required | Description | Default |
|---|---|---|---|
--primer_seq |
Yes | File with primer sequences | NA |
--product_size_max |
No | Maximum amplicon size | 2000 |
--req_five |
No | Require 5' end binding | True |
--output_fasta |
No | Output amplicons in FASTA | False |
--exclude_primers |
No | Exclude primers from FASTA output | False |
Output Files
Multiplex Primer Design
MultiPlexPrimerSet.xlsx: Contains primer pairs, Tm values, and product sizesMultiPlexPrimerSet_amplicons.fasta: (Optional) FASTA file of amplicon sequences
In Silico PCR
in_silico_PCR.xlsx: Excel workbook with multiple sheets:amplicons: Predicted PCR productsdimers: Potential primer-dimer interactionsinteractions: Cross-reactions between amplicons
in_silico_PCR_amplicons.fasta: (Optional) FASTA file of predicted amplicons
The FASTA output files contain:
- Headers in format:
>target_name_start_end_length - Sequences either:
- Include primers (default)
- Exclude primers (with
--exclude_primers)
Testing Recommendations
When validating primers for diagnostic assays:
- Perform qPCR with individual primer pairs
- Use EVA Green plus (20X in water) and ROX (50X)
- Analyze melt curves
- Confirm single bands via agarose gel electrophoresis
Online Version
A web version of primerJinn's getMultiPrimerSet is available at DrDx.Me
Citation
Limberis, J.D., Metcalfe, J.Z. primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR. BMC Bioinformatics 24, 468 (2023). https://doi.org/10.1186/s12859-023-05609-1
Author
Jason Limberis (JasonLimberis@ucsf.edu)
License
This project is licensed under the MIT License.
1 maintainer
Metadata
1 maintainer
Release files for primerJinn 2.0.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| primerjinn-2.0.3.tar.gz | 16.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| primerjinn-2.0.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 32.4 kB
Release files / primerjinn-2.0.3.tar.gz
| Download URL | primerjinn-2.0.3.tar.gz |
|---|---|
| Size | 16.8 kB |
| Tags | Source |
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