Hi Saleh, I realize this reply is coming quite late. Hopefully it is still useful. more below...
On Wed, 2014-06-18 at 09:43 +1000, Saleh T wrote: > I used progressivemauve to compare two genomes each saved in the fasta > file format. In each genome file there are more than one sequence > corresponding to the chromosomes. I read in the manual that fasta file > containing multiple sequences will be merged together. > > > I have two questions: > > > 1) Where do I find the LCBs? Running progressive generated 3 files > (.xmfa, .bbcols, and .backbone). From reading the manual and this > forum I had a feeling that the LCBs are located in the backbone file. > However the backbone file has a lot of records while when I visualize > the alignment from the mauve interface it says there are only few > thousands LCBs, a number way low compared to the records in the > backbone file. Could someone please clarify this? When using 3 or more genomes and permitting alignments among subsets of the genomes, the LCBs can become (mathematically) ambiguous to define, e.g. the same alignment could yield multiple alternate sets of LCBs. Thus the LCB concept is only well-defined in the context of pairwise alignment or core genome alignment (where only content shared by all N genomes is aligned). > > > > 2) Since my interest is on finding the LCBs, how do I go back to find > out where these LCBs are located in the genome after the chromosome > sequences have been merged together? Currently the coordinates seen on > the backbone file are irrespective of the chromosome sequence. > Given the aforementioned issue I think we need to know more about what you're hoping to achieve before it's possible to suggest how to get there with the progressiveMauve outputs. -- 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. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
