OrchidBase: comparative genomics of synteny and miRNA-target gene among orchid whole genomes

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Student thesis: Doctoral Thesis


Orchidaceae are the largest families of flowering plants and most important ornamental plants Considering the importance of Orchidaceae research in Orchidaceae and breeding communities should have access to useful genomic and transcriptomic information Recently National Cheng Kung University have sequenced the whole genome of Phalaenopsis equestris Dendrobium catenatum and Apostasia shenzhenica For the convenience of further research OrchidBase was established by collecting all the information of the sequenced data into a database This study is divided into three part The first part is about miRNA target prediction Using the machine learning method we can predict the position of mature miRNA Then we use TAPIR algorithm to predict the target of miRNA To increase the reliable of research result we use a lot of characteristic of miRNA The second part is synteny viewer We defined the synteny blocks by the definition in previous paper and visualize the data by web tools User can simulate the experiment by using our tools to reduce the cost of the actual experiment Final part is gene order viewer Using the algorithm to compare different sequences and the features of gene duplicate visualize the gene sequences and convent the researchers to study the evolution of different genes
Date of Award2020
Original languageEnglish
SupervisorWei-Sheng Wu (Supervisor)

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