Restriction enzyme mining for SNPs in genomes.
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.
Chuang
Li-Yeh
LY
Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan, ROC.
Yang
Cheng-Hong
CH
Tsui
Ke-Hung
KH
Cheng
Yu-Huei
YH
Chang
Phei-Lang
PL
Wen
Cheng-Hao
CH
Chang
Hsueh-Wei
HW
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*
D004262:DNA Restriction Enzymes