Analysis of Gene Expression Data Spring Semester , 2004

This work by Pe'er et al. [5] presents an algorithm for reconstructing a target sequence using the SBH technology integrated with known similar reference sequence. The goal is to get the best reconstruction, given these two sources of information. Some motivation for using the method: tests are performed separately for each mutation with different technologies. Since we know the sequence of the gene (and sometimes even where the mutation might appears) we would like to use this information for finding the correct path of the SBH output. • Identifying unknown microorganism can be done by the sequence of a conserved known gene. • Identifying a specific strain by more divergent sequences. • Finding the gene's sequence in one species, given this gene's sequence in another species. • HLA-typing (graft recognition). • Detecting somatic mutations (cancer). All those challenges present one common problem: we need to reconstruct a target sequence given a known similar reference sequence. Current technologies are either target-specific, or ignore existing information on target (redo sequencing the target).