SeqAn Seeds Update

13. March 2013

The SeqAn team is happy to announce the update of the seeds module.

The previous seeds module had numerous problems, including memory leaks and bugs. We have rewritten the seeds module such that it now supports a more handy interface while removing the bugs and the problems of the previous one. The new version is based on the interim module seeds2. We have adapted the interfaces to better match the contents of the whole library, especially with the updated alignment module.

The new seeds module features:

  • A basic implementation of the SeedSet class. A more refined version will follow shortly.
  • An updated interface for the Seed class for local chaining and its specializations.
  • An updated version of the global chaining algorithm.
  • A greatly updated and improved version of the banded chain alignment module based on the new alignment module.

The API documentation has already been updated to provide documentation for the new module. We are currently in the process of  updating the Seed-and-Extend tutorial.

We are certain that the updates are a great improvement over the old seeds module and hope that the update does not cause too much inconvenience.

Have fun with the new seeds module!

Last Update 13. March 2013