ArticleNucleic acids research2009
TmPrime: fast, flexible oligonucleotide design software for gene synthesis.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A Physics-Inspired Approach to Improve Oligonucleotide Design and Gene Synthesis.Computational and structural biotechnology journal · 2026Article
- Design and structure of overlapping regions in PCA via deep learning.Synthetic and systems biotechnology · 2025Article
- CertPrime: a new oligonucleotide design tool for gene synthesis.Computational and structural biotechnology journal · 2025Article
- A depth-first search algorithm for oligonucleotide design in gene assembly.Frontiers in genetics · 2022Article
- An Integrated Algorithm for Designing Oligodeoxynucleotides for Gene Synthesis.Frontiers in genetics · 2022Article
- Optimization of the experimental parameters of the ligase cycling reaction.Synthetic biology (Oxford, England) · 2019Article
- A Dual-Replicon Shuttle Vector System for Heterologous Gene Expression in a Broad Range of Gram-Positive and Gram-Negative Bacteria.Current microbiology · 2018Article
- High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment.Scientific reports · 2017Article
- BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.Bioinformatics (Oxford, England) · 2016Article
- Primerize: automated primer assembly for transcribing non-coding RNA domains.Nucleic acids research · 2015Article
- DNASynth: a computer program for assembly of artificial gene parts in decreasing temperature.BioMed research international · 2015Article
- A critical analysis of codon optimization in human therapeutics.Trends in molecular medicine · 2014Review
- Simultaneous splicing of multiple DNA fragments in one PCR reaction.Biological procedures online · 2013Article
- Computational codon optimization of synthetic gene for protein expression.BMC systems biology · 2012Article
- Computational tools for the synthetic design of biochemical pathways.Nature reviews. Microbiology · 2012Review
- ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.Nucleic acids research · 2011Article
- GeneDesign 3.0 is an updated synthetic biology toolkit.Nucleic acids research · 2010Article
- Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides.Nucleic acids research · 2009Article
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Authors and funding
5 authors.
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Abstract
Herein we present TmPrime, a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences and potential formation of secondary structures. Our program also provides functions on sequence pooling to separate long genes into smaller pieces for multi-pool assembly and codon optimization for expression. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp) using real-time PCR assembly with LCGreen I, which offers a novel approach to compare the efficiency of gene synthesis. The purity of assembled products is successfully estimated with the use of melting curve analysis, which would potentially eliminate the necessity for agarose gel electrophoresis. This program is freely available at http://prime.ibn.a-star.edu.sg.
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