Hi Hannes, Couple of things in response to your mails:
- thanks for providing the example, I have moved it to a Cookbook page, since we had several DNA alignment related questions recently. http://biojava.org/wiki/BioJava;CookBook3:PSA_DNA - I believe the AmbiguityDNACompoundSet is required, to match the compound set of the substitution matrix. - about your sequence matching strategy: this really depends on your size and similarity of DNA sequences. if you have many, then blast might be the way to go, otherwise just looking a number of identical positions (psa.getNumIdenticals()) might be a quick and dirty solution for this as well. - ConcurrencyTool is just a utility class for working with the Java concurrency framework. Should be easy to write your own Callable classes that do pairwise alignment, if you needs to do this in multiple threads... Andreas _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
