- 期刊
Dynamic Programming for Single Nucleotide Polymorphism Id Identification in Systematic Association Studies
在系統相關性研究中使用動態規劃法找尋單核苷酸多型性身分證(SNP ID)
摘要
單一核苷酸多型性(single nucleotide polymorphisms、SNP)在個人化醫學上扮演很重要的角色。然而，很多關聯性研究對於SNP資訊的描述僅提供SNP核苷酸或胺基酸的位置，而沒有提供NCBI SNP ID。因此，一個能夠提供SNP ID辨識且具有友善使用者介面的工具是必需的。本研究使用動態規劃方法來比對輸入序列與SNP FASTA資料庫間的相似性，並且提出一個基於NCBI dbSNP資料庫的web-based系統，來提供SNP序列辨識和SNP FASTA格式。此系統能夠輸入各種格式的序列，包括一般化的序列格式（如ACGT、[dNTP1/dNTP2]或IUPAC格式）和不同方向的序列。相較於NCBI SNP-BLAST，本研究提出的系統能依照染色體和contig位置提供正確的目標的SNP ID (SNP hit)，而且也能提供鄰近的SNPs (flanking hits)，並且也解決了SNP-BLAST對於輸入序列常常不能夠提供正確SNP ID的問題。因此，我們將動態規劃方法新穎地應用在SNP ID搜尋與辨識，讓使用者可以查詢文獻上的序列及輸入序列中所包含的SNP ID，而提供系統性的相關性研究。這個程式在網頁http://bio.kuas.edu.tw/SNPosition/可以免費使用。
並列摘要
Single nucleotide polymorphisms (SNPs) play an important role in personalized medicine. However, the SNP data reported in many association studies provide only the SNP nucleotide/ amino acid position, without providing the SNP ID recorded in National Center for Biotechnology Information databases. Atool with the ability to provide SNP ID identification, with a user-friendly interface, is needed. In this paper, a dynamic programming algorithm was used to compare homologs when the processed input sequence is aligned with the SNP FASTA database. Our novel system provides a web-based tool that uses the National Center for Biotechnology Information dbSNP database, which provides SNP sequence identification and SNP FASTA formats. Freely selectable sequence formats for alignment can be used, including general sequence formats (ACGT, [dNTP1/dNTP2] or IUPAC formats) and orientation with bidirectional sequence matching. In contrast to the National Center for Biotechnology Information SNP-BLAST, the proposed system always provides the correct targeted SNP ID (SNP hit), as well as nearby SNPs (flanking hits), arranged in their chromosomal order and contig positions. The system also solves problems inherent in SNP-BLAST, which cannot always provide the correct SNP ID for a given input sequence. Therefore, this system constitutes a novel application which uses dynamic programming to identify SNP IDs from the literature and keyed-in sequences for systematic association studies. It is freely available at http://bio.kuas.edu.tw/SNPosition/.
延伸閱讀
- 孫心慈、莊旻傑（2020）。電化學式單核苷酸多態性感測發展與應用。化學，78(1)，21-34。https://doi.org/10.6623/chem.202003_78(1).003
- 平嘉雲、吳東鴻、李長沛、賴明信（2012）。運用酶切差異設計單一核苷酸多型性分子標誌。技術服務，23(3)，19-22。https://doi.org/10.29571/ZHWHGX.201209.0005
- Wang, C. (2015). 利用漢明距離偵測單一核苷酸多型性之群聚與單一核苷酸多型性集合之相關性檢定 [doctoral dissertation, National Taiwan University]. Airiti Library. https://doi.org/10.6342/NTU.2015.02422
- 梁超（2011）。應用跨研究之單核苷酸多態性標記子以建立整合性遺傳風險預測模型〔碩士論文，國立交通大學〕。華藝線上圖書館。https://doi.org/10.6842/NCTU.2011.00656
- 方武祥（2009）。開發比較對照組和控制組之單核苷酸多型性的生物資訊系統〔碩士論文，國立臺北大學〕。華藝線上圖書館。https://www.airitilibrary.com/Article/Detail?DocID=U0023-0709200900000700