Let me preface this by saying that the particular dataset is not one that you would use mauve for in reality, and thus I can be dismissed as asking a stupid question ...
That said, in the context of quickly comparing some alignment tools I had a user come across a dataset that puts mauve into an essentially infinite loop -- except for occasional crashes, progressive mauve is happy to churn for as long as you are willing to let it, producing no result (the longest actual time was 2.5 hours). Looking at the console, it seems to be stuck looking for the LCBs when the sequences are too short and dissimilar. I naively would have thought that situation would result in a more graceful exit, possibly with a notice of insufficient similarity. I told the user that mauve was just not the right tool, but is this at all indicative of an actual issue? The sequences are (remember, I said they were too short to really use with mauve): >chimp.Rp1.exon3 gttcccagcctccaggcagtgatcctgagctctggagctgtggtggcggcaggaagggag ccatttaaaccaggaaattatgacatccaaaaatacttgcttcctgctagattaccaggg atctctcagcgtgtgtaccccaagggaaatgcaaagtcagaaagcagaaaga >cow.Rp1.exon2 gttcccagtctgcaggctgtgatcctgagctctggagctgtggtggcagcaggaagggaa ccgtttaaaccaggaaattatgacatccaaaagtacttgcttcctgctagattaccaggc atctctcgtcgtgtgtaccccaagggaaatgctaggtcagaaagcagaaaaa >dog.Rp1.exon2 gttcccagtctccaggcggtgatcctgagctctggagctgtggtggcagcaggaagggag ccatttaaaccaggaaattatgacatccagaagtacttgctttctgcaagattaccaggg acctctcatcatgtatacatcaagggaaatactagatcagaaagcagaaaga >AF291754 gtgagctacttctggagattaacatcaccttggattaaattaattggctgtacttaatct gtgagcacacatgctagtaataaatccaaagacatttgtttacgtgaaacaagcaggttg catatccagtgacgtttatacagaccacacaaactatttactcttttcttcgtaaggaaa ggttcaacttctg >rat.Rp1.ex3 gttcctagtctccaagcagtgatactgagctctggagctgtggtggcagccggaagggag ccattcaaaccaggaaattacgacatccaaaaatacttgcttcctgtcaagttaccagga atctctcatcgcgtgcaccggaagggaaaagccaagatagaaaaaagaaaga >rhesus.Rp1.exon3 tttcaccacagaaacgaaaaggagaggattgaaaaacattctaaactgaaattggctata tttatagttggaaagaatcatggagattatctgtgttttagacttttccaaatcaatgat atgcctgtttaaattgatgatgtgtgctttttttgcataaactacctagtta Cheers, Guy ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
