Converting bisulfite-converted sequence back to genomic sequence

Question

[sp16027]

Good afternoon,

Can anyone recommend a tool/way to convert published bisulfite-converted target sequences back to genomic sequences? I am trying to locate published pyrosequenced regions in the rat genome to identify candidate genomic regions and design my own prosequencing assays around them

Many thanks,

Silvia

Answer 1

[Devon Ryan]

It's a crappy solution, but you can "simply" use a bisulfite aligner (bwameth, bismark, etc.) to create the index and align the sequences. There's probably a more efficient blast-based way of doing that for small numbers of sequences, but it'll get the job done.