Single nucleotide polymorphisms (SNPs) are responsible for much of the genetic variation within our species. This tutorial demonstrates how to find information about SNPs in different databases and some points to consider when deciding whether a discrepant base might be a SNP or an experimental error.

Programs and databases shown in this tutorial are from the National Center of Biotechnology Information (NCBI), the National Cancer Institute (NCI), and Geospiza, Inc.

The first section of this tutorial shows how sequence analysis programs, such as phred and phrap, can be used to measure sequence quality and distinguish potential SNPs from potential errors. The second part shows three ways to determine if a SNP has already been found. Lastly, example sequences are provided from contigs that can be used for SNP hunting.

1. Identity potential SNPs by using information about sequence quality. In this example, trace files were loaded into Geospiza's Finch^®-Server, analyzed by Phred, and assembled with Phrap as part of the Finch-Server pipeline.

2. Determine if a SNP has been previously identified by using blastn to compare a sequence to one of three different databases.

A. GenBank (the non-redundant nucleotide sequences)

B. dbSNP (NCBI's SNP database)

C. The NCI CGAP SNP index

• BLAST (http://www.ncbi.nlm.nih.gov/BLAST)
• BLAST dbSNP(http://www.ncbi.nlm.nih.gov/SNP/snpblastByChr.html)
• CGAP SNP index (http://lpgws.nci.nih.gov:82/perl/snpbr)
• Additional SNP information can be found at The SNP Consortium site at Cold Spring Harbor

Before you begin, here are some helpful hints: