For decades DNA Methylation had been thought to play an important role in gene expression. When DNA is treated with bisulfite, any cytosines are converted to uracil unless the cytosine has been methylated. GSNAP(1) aligns the next-generation sequencing reads taken from bisulfite treated DNA sequencing to a reference sequence, aligning them in a manner which does not obscure genuine mismatches but still exposes the C to T mismatch which occurs when unmethylated DNA is treated with bisulfite.
(1) Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26: 873-881