title: Restriction enzyme mining for SNPs in genomes.
abstract: 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.
authors.affiliation: Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan, ROC.
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.forename: Ke-Hung
authors.initials: KH
authors.lastname: Tsui
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: Phei-Lang
authors.initials: PL
authors.lastname: Chang
authors.forename: Cheng-Hao
authors.initials: CH
authors.lastname: Wen
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000818:Animals; D004262:DNA Restriction Enzymes / Q000378:metabolism; D016678:Genome; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D015183:Restriction Mapping / Q000379:methods*
chemical_list: D004262:DNA Restriction Enzymes