TmPrime: fast, flexible oligonucleotide design software for gene synthesis

TmPrime: fast, flexible oligonucleotide design software for gene synthesis

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 ...

A fast and flexible approach to oligonucleotide probe design for genomes and gene families

A fast and flexible approach to oligonucleotide probe design for genomes and gene families

MOTIVATION With hundreds of completely sequenced microbial genomes available, and advancements in DNA microarray technology, the detection of genes in microbial communities consisting of hundreds of thousands of sequences may be possible. The existing strategies developed for DNA probe design, geared toward identifying specific sequences, are not suitable due to the lack of coverage, flexibilit...

Gene2Oligo: oligonucleotide design for in vitro gene synthesis

There is substantial interest in implementing a bioinformatics tool that allows the design of oligonucleotides to support the development of in vitro gene synthesis. Current protocols to make long synthetic DNA molecules rely on the in vitro assembly of a set of short oligonucleotides, either by ligase chain reaction (LCR) or by assembly PCR. Ideally, such oligonucleotides should represent both...

Flexible Software Framework for Modal Synthesis

Modal synthesis is an important area of physical modeling whose exploration in the past has been held back by a large number of control parameters, the scarcity of generalpurpose design tools and the difficulty of obtaining the computational power required for real-time synthesis. This paper presents an overview of a flexible software framework facilitating the design and control of instruments...