SNP-flankplus: SNP ID-centric retrieval of flanking sequences

Abstract

PCR is essential for many single nucleotide polymorphism (SNP) genotyping methods. However, the flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus making the design of appropriate PCR primers difficult. Here, we provide the system design and algorithm to describe a tool named "SNP-Flankplus" to provide a web environment for retrieval of SNP flanking sequences from both the dbSNP and the nucleotide databases of NCBI. SNP rsID# and ssID# are acceptable for retrieval of the SNP flanking sequences with adjustable lengths for at least sixteen organisms. © 2009 Springer-Verlag Berlin Heidelberg.