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SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

Hsueh-Wei Chang1234, Yu-Huei Cheng5, Li-Yeh Chuang6* and Cheng-Hong Yang57*

Author Affiliations

1 Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan

2 Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan

3 Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan

4 Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan

5 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan

6 Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan

7 Department of Network Systems, Toko University, Chiayi, Taiwan

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BMC Bioinformatics 2010, 11:173  doi:10.1186/1471-2105-11-173

Published: 8 April 2010

Abstract

Background

PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2.

Results

The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system.

Conclusions

The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2 webcite.