De Novo Gene Synthesis Design Using TmPrime Software View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2012

AUTHORS

Mo-Huang Li , Marcus Bode , Mo Chao Huang , Wai Chye Cheong , Li Shi Lim

ABSTRACT

This chapter presents TmPrime, a computer program to design oligonucleotide for both ligase chain reaction (LCR)- and polymerase chain reaction (PCR)-based de novo gene synthesis. The program divides a long input DNA sequence based on user-specified melting temperatures and assembly conditions, 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 in a PDF file, which will be sent to the user via e-mail. The program also provides functions on sequence pooling to separate long genes into smaller pieces for multipool assembly and codon optimization for expression based on the highest organism-specific codon frequency. This software has been successfully used in the design and synthesis of various genes with total length >20 kbp. This program is freely available at http://prime.ibn.a-star.edu.sg. More... »

PAGES

225-34

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-61779-564-0_17

DOI

http://dx.doi.org/10.1007/978-1-61779-564-0_17

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1002797519

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22328437


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