Hi Norhan, If you need programmatic access to do automated processing, you can use the coordinates in the .backbone file to query an annotation file to get the features at those particular coordinates. Probably BioPython/BioPerl/BioJava or some similar API could help with annotation parsing & queries. Keep in mind that the .backbone file uses a concatenated coordinate system, e.g. the 1st site in the 2nd contig/chromosome has a coordinate which is the length of the 1st + 1, so some logic to convert to contig local coordinates will need to be implemented.
If you just want to explore visually, you should be able to load aligned GenBank format files into the Mauve viewer and zoom in on regions of interest. Best, -Aaron On Thu, 2015-04-02 at 00:03 +1100, Norhan Mahfouz wrote: > Hi, > I am currently analyzing alignment data from 50 bacterial genomes after > applying progressive mauve for the alignment. > I am processing the backbone file and I was wondering how can I > integrate annotation information to this knowledge, for example : from > the backbone file seq1 and seq5 have in common a stretch of nucleotides > from 11658 to 11768 and 12340 to 12450 respectively - one can extract > the actual string of nucleotides from the xmfa file, sure > If I am using the annotated genomes, how can I extract which genes does > this area belong two on each of the respective genomes?? > Your input and ideas are highly appreciated! > regards, > Norhan > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
