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SeeSNP Propietary Analysis Advantages

To accelerate the data analysis process, we have developed a reviewing interface that integrates with our Oracle database. This interface assists the reviewers by: 1) marking the exonic regions of the amplicons and reporting any SNPs that result in amino acid changes; 2) remapping the amplicon SNP coordinates to the base coordinate on the mRNA; 3) annotating Pfam domains so a user can quickly assess if the SNP is in a critical protein domain; 4) referencing dbSNP to determine if the SNP has been previously reported; 5) displaying the likelihood of heterozygosity; 6) providing SNP frequency in the population; and 7) providing a three-tier manual reviewing and version control system. The optional manual reviewing system records and tracks edits to any SNP calls or score change made by the three individual manual reviewers.

A software program cannot be universally successful if it fails to account for the diverse and relatively frequent spectrum of polymorphisms and context-related sequencing artifacts that occur. PolyPhred can be an extremely valuable and highthroughput tool for SNP discovery if it is applied in a heuristically- controlled manner to account for such artifacts.

The core component of PolyPhred that calculates the likelihood of heterozygosity by evaluating multicomponent signals is well tested, easily automated, and highly reliable. The input quality files can be corrected for known sequencing artifacts, enabling the implementation of a very powerful automated analysis system.

The final frontier for automated SNP discovery is to be able to identify which reads contain heterozygous insertions or deletions, and then to resolve their genotypes. Trace subtraction
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