Hi Andrés... Andrés Fernando Cubillos Ruiz wrote: > Hi Aaron, > > I have used Progressive Mauve in order to compare closely related intraspecies > bacterial genomes and it works perfect in predicting the few rearragements > that > those genomes have suffer, even the ones that the previous versions of Mauve > couldn´t detect. When aligning with Progressive Mauve I don´t find any islands > file in the output files, since the data structure of the .islands file is > very > helpful to my analysis I would like to know how I can get the islands file > resulting from the alignment with the Progressive version?. >
As you noticed, Progressive Mauve isn't generating an islands file. You may also have noticed that the .backbone file generated by progressiveMauve has a very different format than the original mauveAligner backbone file. The new .backbone file contains information on "subset backbone" and is essentially a complete catalog of the coordinates of every conserved segment in the aligned genomes. The regions not identified in the .backbone file can be considered genome-specific regions, or islands. progressiveMauve does not currently create an output file listing such coordinates, but it should be possible to process the backbone file with a spreadsheet like excel or OpenOffice to get the set of island coordinates. In any case, I've added .islands file output for progressiveMauve as a feature request in our sourceforge tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=1657710&group_id=181544&atid=897630 ------------------------------------------------------------------------- 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
