Development of a program to analyze the single nucleotide polymorphism of multiple sequence chromatography.

• Main Authors: Hsuan-Hung Shen, 沈宣宏
• Other Authors: Yun-Shien Lee
• Format: Others
• Language: zh-TW
• Published: 2013
• Online Access: http://ndltd.ncl.edu.tw/handle/20851280761630369350

碩士 === 銘傳大學 === 生物科技學系碩士班 === 101 === Using bioinformatics to explore the human genomic polymorphism could save the time and costs, when we have a massive study in the multiple sequences analysis. There are four type of human genomic polymorphism: Single Nucleotide Polymorphism (SNP), Insertion and Deletion (Indel), Short Tandem Repeat (STR) and Copy Number Variations (CNV). Traditional, we analyze the SNPs of the sequence chromotograpy (the .ab1 file, generated with ABI sequencer) with freeware Chomas or commerce software Vector NTI Advance program. However, both software still relies on manual visualization to find the SNPs, and cannot judge SNPs base automatically. Both softwares are also lack of relevant SNPs annotation features. In this study, we used the Matlab programming language, to develop a detect software: Sequence Analyzer, to analyze SNPs variation for multiple samples sequence data (multiple sequence chromatography). Sequence Analyzer can automate analyze the SNP variants of the multiple samples sequencing, it also can obtained the SNPs annotation information through the UCSC Genome Browser database. In this study, we would describe the development and algorithm of the program. We also compare the Sequence Analyzer with several traditional SNP analysis softwares. I hope this software can help the development for human genomic study.