Hi Anastasia, On Mon, 2010-06-21 at 19:55 +0200, Anastasia Gioti wrote: > hello, > I was wondering whether it is possible to give MAUVE a file different > from a genbank file in case one wants to load annotations on the > aligned genomes. I find this particularly useful when looking at my > synteny blocks, but I don't have genbank files for most of my genomes. > I have gff files from annotations made with MAKER, but I don't see > that option in the manual. Maybe in the command line version? > I also tried to create genbank -type files ( i don't want to submit > yet) but although these loaded successfully, I only see the name of > the scaffold, not related features. My way of creating genbank-type > files may be too rough (i don't know how to really do it, used > DNAnnotator and merged output files) but it does create a features+ > sequence file (though features are all annotated as exons). Any help > would be appreciated!
Currently the Mauve GUI only fully supports GenBank for sequence annotation viewing. However, the GUI only shows the following feature types by default: CDS, tRNA, rRNA, misc_RNA, and repeat_region. Notice that exon is not in that list. So if you change all exon annotations to CDS, for example, they should appear in the GUI. As for other formats, there is partial support for INSDseq XML format, and using it requires editing the XMFA file to indicate that the AnnotationFormat is INSDseq. The command-line aligner can not parse the XML, but the GUI can display the above-listed feature types from XML. At some point it would be great if the GUI was more configurable and flexible with annotation viewing, it's something us Mauve developers have been planning for a while but haven't been able to push out in a release yet for various reasons. Hope that helps, -Aaron ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
