A novel method providing exact SNP IDs from sequences

摘要

Single nucleotide polymorphisms (SNPs) are the most frequently occurring genetic variations. Biologists use identified SNPs to investigate genetic diseases; current heredity markers, as well as to prevent side effects of medication. Thus, SNPs play an important role in personalized medicine. However, many association studies provide only the relationship between SNPs, diseases and cancers, without giving an SNP ID. In order to identify SNPs in a sequence, this research built dbSNP, SNP fasta and SNP flanking marker databases for the rat, mouse and human genome from the NCBI database. It utilizes SNP flanking markers that are extracted from a SNP fasta sequence and the combines them with a Boyer-Moore algorithm with a dynamic programming method to match unknown sequences with data from the NCBI SNP fasta sequence database to retrieve SNP IDs. The experimental results show that this method is indeed able to determine the exact SNP IDs from sequence. It constitutes a novel application to identify SNP IDs from the literature and can be used systematic association studies.