Our work in this project is centered on the idea of tackling the problem of determining methylation landscapes using alignment algorithms especially designed for BS-treated sequences. Opposed to most of the available tools for such king of alignment, we are developing a module for our aligner rNA that will not work with a reduced alphabet but, instead, uses an extended one. Using a weighted Hamming distance (dinamically varying along the genome) we try to improve precision, especially in regions with a low level of methylation. Among further directions of investigation, we mention a systematic comparison of alignments of sequences produced with different technologies (e.g. 454), and the integration of alignment and structural variation analysis.