Hi Lee, Glad to hear you are having some success with Mauve! more below... Lee Larcombe wrote: > Anyway, the results are encouraging, but I have an aesthetic problem! As the > genomes are circular the sequence starts at different places for different > genomes. Although this does not affect the alignment, it does mean that I > get a complete mess of lines joining up alignment blocks in the graphical > display. > > Is there any function within Mauve to set the start point of the sequence to > align (I assume not - I can't find one), or horizontally scroll the > graphical display of one genome relative to the others? Alternatively, do > you know of another tool which could do this before I align? I could write > some perl to reorder the sequences, but I'm sure someone must have faced > this problem before! >
The two solutions you have suggested both sound reasonable, but at the moment Mauve doesn't offer an implementation of either. Yes, it seems that modifying the coordinate system for circular genomes must be a common problem, and I'm sure software must exist to modify GenBank or FastA files in such a way, but my quick google searches didn't turn anything up. If you happen to find or write some software to do this, please let the world know. After processing the sequence data file it would be necessary to re-run the alignment, of course. It would be great to be able to remap the display coordinate system that Mauve uses for circular chromosomes on-the-fly, and I have added this as a feature request in our sourceforge tracker so we don't lose sight of the idea: https://sourceforge.net/tracker/index.php?func=detail&aid=1657714&group_id=181544&atid=897630 -Aaron ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
