Restriction enzyme mining for SNPs in genomes

Li Yeh Chuang, Cheng Hong Yang, Ke Hung Tsui, Yu Huei Cheng, Phei Lang Chang, Cheng Hao Wen, Hsueh Wei Chang

研究成果: 雜誌貢獻文章同行評審

43 引文 斯高帕斯(Scopus)

摘要

Many different single nucleotide polymorphisms (SNPs) genotyping methods have been developed recently. However, most of them are expensive. Using restriction enzymes for SNP genotyping is a cost-effective method. However, restriction enzyme mining for SNPs in a genome sequence is still challenging for researchers who do not have a background in genomics and bioinformatics. In this review, the basic bioinformatics tools used for restriction enzyme mining for SNP genotyping are summarized and described. The objectives of this paper include: i) the introduction of SNPs, genotyping and PCR-restriction fragment length polymorphism (RFLP); ii) a review of components for genotyping software, including tools for primer design only or restriction enzyme mining only; iii) a review of software providing the flanking sequence for primer design; iv) recent advances in PCR-RFLP tools and natural and mutagenic PCR-RFLP; v) highlighting the strategy for restriction enzyme mining for SNP genotyping; vi) a discussion of potential problems for multiple PCR-RFLP. The different implications for restriction enzymes on sense and antisense strands are also discussed. Our PCR-RFLP freeware, SNP-RFLPing, is included in this review to illustrate many characteristics of PCR-RFLP software design. Future developments will include further sophistication of PCR-RFLP software in order to provide better visualization and a more interactive environment for SNP genotyping and to integrate the software with other tools used in association studies.
原文英語
頁(從 - 到)2001-2007
頁數7
期刊Anticancer Research
28
發行號4 A
出版狀態已發佈 - 7月 2008
對外發佈

ASJC Scopus subject areas

  • 腫瘤科
  • 癌症研究

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