A cross-species EST-based pipeline for identification of exons and alternatively spliced variants

• Main Authors: You-Wei Wang, 王宥崴
• Other Authors: Trees-Juen Chuang
• Format: Others
• Language: zh-TW
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/00049551379068723021

碩士 === 國立臺北大學 === 資訊工程學系 === 102 === Alternative splicing (AS) is a major post-transcriptional mechanism for producing multiple mRNA isoforms from a single precursor mRNA, thereby increasing the complexity of the transcriptome/proteome. AS is widespread in eukaryotes, and it has been suggested that over 95% of genes in human and over 60% genes in plants are alternatively spliced. However, current gene annotations may contain certain false-positive predictions and alternatively spliced variants (ASVs) that are functionally irrelevant. Since high sequence similarity reflects functional conservation, we designed an evolutionarily-conserved expressed sequence tags (ESTs)-based pipeline to identified previously-uncharacterized exons/ASVs and thus reannotated the specified species. In this thesis, we applied to crop gene annotations and successfully identified 7704 previously-uncharacterized ASVs (exons) in rice from ESTs of nine grass plant species. Then, we used ESTs of six primate species to find out 1773 previously-uncharacterized ASVs in human. The use-friendly interface with visualization is also provided.