On Wed, 2006-02-22 at 17:48 -0700, Nick Robertson wrote: > If you could please post your input query and the results file produced by MPT, > I will re-run this experiment and attempt the reproduction of these results. Sure: http://www.broad.mit.edu/personal/jcuff/mpt/ The result file has the same name as the files on your system I ran a couple of hours ago. It's a pretty noddy test, I don't have the time to do any more sorry. I see two issues that could stop uptake by a wide audience right now: 1. The sub alignments are not being reported. This will make your code go fast, but having given the data a quick once over I'm sure this is where you are missing alignments. 2. The blast format output could not be parsed without modifying it first, although this is easy for you to fix. I only noticed it when starting to check the results. Sorry most bioinformatics is parsing and data munging, boring but it needs to be done. Anyway, the results are up for all to see, hope you can work round these wrinkles. Thanks for being open about this Nick, I'm sure you'll get through the teething issues, it's still early days for the product. I'm all done, if others in the group want to take this further then cool, but I'm bowing out now. Best, J.