PD5: A General Purpose Library for Primer Design Software

Riley, Michael C.; Aubrey, Wayne; Young, Michael; Clare, Amanda

doi:10.1371/journal.pone.0080156

Cited by 6 publications

(3 citation statements)

References 24 publications

(25 reference statements)

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“…A key step to automating multiple genomic element deletion is development of the bioinformatics algorithms to automate primer design. We developed this “Precise Deletion” software using a modular software library for primer design known as PD5 [ 27 , 35 ].…”

Section: Resultsmentioning

confidence: 99%

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation

et al. 2015

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Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method’s primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

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Section: Resultsmentioning

confidence: 99%

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation

et al. 2015

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“…Toksin yang dihasilkan oleh bakteri C. difficile adalah eksotoksin A (tcdA) dan/atau toksin B (tcdB) yang berperan sebagai faktor virulensi penyebab penyakit. Toksin A bersifat enterotoksin yang dapat merusak mukosa usus dan merangsang pengeluaran cairan, sementara toksin B bersifat sitotoksin yang dapat merusak sel-sel kolon (Riley et al, 2013) Lebih parahnya dapat menyebabkan erosi pada mukosa usus dan merangsang pengeluaran cairan dari usus, selain itu toksin ini juga dapat menyebabkan perdarahan (Putri, 2015).…”

Section: Pendahuluanunclassified

“…Ukuran produk primer yang diperoleh memiliki rentang antara 150-248 bp. Menurut (Riley et al, 2013) ukuran produk yang ideal antara 80-300 basis, sehingga ukuran produk primer memenuhi syarat ideal.…”

Section: Tabel 1 Hasil Rancangan Desain Primer Menggunakan Primer3plusunclassified

DESAIN PRIMER SECARA IN SILICO UNTUK AMPLIFIKASI GEN tcdA BAKTERI CLOSTRIDIUM DEFFILCILE

Dewi,

Octifani

2023

JALM

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Antibiotics are drugs used to fight infections caused by bacteria. C. difficile bacteria is a bacterium that causes Clostridium difficile infection (ICD). Toxin A of C. difficile bacteria is exotoxin A (tcdA) which is a virulence factor that causes disease. Toxin A can damage the intestinal mucosa and cause bleeding. The cost of examining and treating patients with AAD and PMC is very high, so the dosage must be determined correctly. Laboratory tests function to determine the presence or absence of an ICD. The discovery of specific biomarkers is a discovery priority to improve the quality of laboratory tests. Specific primary design is an important step in all types of laboratory examination methods, one of which is molecular examination by PCR. The primary design must have specific properties so as to be efficient at target amplification. This study aims to obtain a primer design that can be used to limit the amplification area of the TcdA gene in silico. This study used a literature study from the NCBI genbank to obtain the tcdA gene sequence of C. defficile bacteria with accession number DQ902560.1. The tcdA gene sequence of C. difficile bacteria was analyzed using Primer3Plus to determine whether there is hairpin and dimer formation. Furthermore, identification was carried out using web-based in silico PCR to determine the number of amplicon and visualization on the electrophoretic gel. The level of tcdA gene homology in the species group in the BLAST test. The results showed that the best primer design for in silico detection of the tcdA gene of C. difficile was the forward primer 5'-GCAGATGCCAAGAGACACAC-3' and the reverse primer 3'-GCAGATGCCAAGACACACAC-5'. The primary design is able to amplify the tcdA gene region with a size of 247 amplicons.

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Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat

et al. 2020

Theor Appl Genet

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PD5: A General Purpose Library for Primer Design Software

Cited by 6 publications

References 24 publications

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation

DESAIN PRIMER SECARA IN SILICO UNTUK AMPLIFIKASI GEN tcdA BAKTERI CLOSTRIDIUM DEFFILCILE

Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat

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