In Silico Characterization and Primer Design of Thaumatin-Like Protein (TLP) Gene in Kelampayan

Muhammad Dzikri A’zim, Ramli (2022) In Silico Characterization and Primer Design of Thaumatin-Like Protein (TLP) Gene in Kelampayan. [Final Year Project Report] (Unpublished)

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Abstract

Neolamarckia cadamba which is generally known as Kelampayan is a large and sturdy tree which has a rapid growth rate. Kelampayan provides many benefits and uses, ranging from the timber industry, carpentry, and medicinal properties. The problem statement for this study is the lack of genetic information regarding the function of thaumatin-like protein (TLP) in Kelampayan. There are two objectives of this study, firstly is the characterization of TLP gene in Kelampayan by using in silico method for further understanding of the gene. The second objective is to design a primer of TLP gene for many uses such as PCR. The methodology of this study was done in two sections with the first section being the in silico characterization of TP gene. The characterization consists of the phylogenetic tree analysis using MEGA 11 Software, the Domain search using CD Search tool, and Motifs search using MEME Online Tool. The second section, primer design was designed using Primer Blast tool. From 50 TLP nucleotide sequences, the phylogenetic tree shows three distinct groups of TLP, differentiated by their function in their respective species. The primer design also provides the most suitable primer for every nucleotide sequence of TLP in Kelampayan. From this study, the genetic information of TLP was understood greatly from the characterization process and the primer was designed successfully.

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