Hi Mathieu, It sounds like you've successfully aligned a draft genome to a reference sequence obtained from GenBank FTP. If you haven't already, you can use the .gbk files available from the GenBank FTP to get a display of the reference genome annotation in the Mauve GUI.
It sounds like you might want to copy annotation from the reference to the draft genome. Mauve doesn't provide a straightforward way to do that at the moment. It would probably require some custom scripting on your part, but bioperl has an XMFA format parser that may help. Of course the usual cautionary words regarding copying of annotations applies. The task of extracting sequence regions surrounding the contig boundaries and designing primer pairs is also not yet implemented in Mauve, and again I'd suggest some custom scripting with bioperl or another toolbox. The libMems library provides a C++ based interface to programmatically manipulating alignments. Alternatively if there are only a small number of regions you'd like to inspect, it's possible to simply zoom in the Mauve display all the way in to the sequence level to observe the nucleotide sequence near the contig boundaries. The keyboard shortcuts for scrolling (Control + left, right arrows) and zooming (Control + Up, Down) the display may help keep your patience alive a bit longer. Hope that helps, -Aaron On Thu, 2010-08-12 at 14:53 -0400, Mathieu Parent wrote: > Hi ! > > Thanks in advance for the help through the mailing list ! > > I have two bacterial genomes I aligned using the files from the > genbank FTP. Then I have about 100 contigs that I align on the known > genomes in order to retreive any variable sequences to design strain > specific qRT-PCR primers. > > I have aligned everything properly, but now I would like to add the > annotation to the alignment and also extract the sequences from these > variable regions in order to work with them. > > I have no clue how to do both those things ! I run Mauve on my Mac and > I also have access to a linux server box. > > Thanks in advance ! > Regards, > Mathieu > McGill University > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
