Dear Aaron, I recently started using progressiveMauve to align large eukaryotic genomes and ran into some problems:
1) the studied genomes are repeat masked (i.e. contain long stretches of Ns). When extracting homologous segments of the input genomes from the backbone file I found that some are located in masked regions. Is there a way to prevent Mauve from using masked regions in identifying homologous segments? As far as I am aware, no such parameter exists for the incorporated muscle sequence aligner. 2) I observe sometimes strange lines in the backbone file such as the following: ___ 7691835 7691966 -85715547 -85715547 0 0 0 0 349474437 349474583 -700243823 -700243822 0 0 8282300 8282275 0 0 0 0 0 0 0 0 0 0 0 0 ___ Note that in the first line, the segments specified by columns [3,4] and [11, 12] have lengths 0 and -1, respectively. Negative lengths mostly occur for segments that are not homologous to segments in other genomes, as shown in the second line (which makes me wonder why they are included in the backbone file in the first place). I am running progressiveMauve with standard parameters. Kind regards, Daniel ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
