You probably know more about the intricate details than I do! I think perhaps one of the more important recent approaches for potentially gapped or slightly mis

You probably know more about the intricate details than I do! I think perhaps one of the more important recent approaches for potentially gapped or slightly mismatched reads is the use of the Burrows-Wheeler transform. http://en.wikipedia.org/wiki/Burrows–Wheeler_transform http://en.wikipedia.org/wiki/Burrows–Wheeler_transform Heng Li wrote BWA based on this, and it seems to handle some of the issues you were wondering about.