Dear all,
I've been struggling to find a solution for this question and have searched all around (including the mauve mailing list) but couldn't find a way to solve that.
Any help is really appreciated.
I've aligned 5 genomes that are split into a bunch of contigs each (one file per genome; more than a sequence in each file), using progressiveMauve in command line mode. Now I'm looking for a way to extract the aligned coordinates per contig.
When looking at the .xmfa file generated by Mauve I couldn't distinguish among the different contigs in each genome, what makes sense since in the documentation it is stated:
However if I do the same alignment using the GUI version of Mauve there is the distinction among contigs in each genome when visualizing the final alignment, which makes me think that somehow that information is stored somewhere inside some other file that not the .xmfa.
Do you know where or how could I cross data among the output files generated by progressiveMauve in order to extract the regions of a singular contig that were aligned?
Thank you very much in advance.
Best regards,
George Condomitti.
I've been struggling to find a solution for this question and have searched all around (including the mauve mailing list) but couldn't find a way to solve that.
Any help is really appreciated.
I've aligned 5 genomes that are split into a bunch of contigs each (one file per genome; more than a sequence in each file), using progressiveMauve in command line mode. Now I'm looking for a way to extract the aligned coordinates per contig.
When looking at the .xmfa file generated by Mauve I couldn't distinguish among the different contigs in each genome, what makes sense since in the documentation it is stated:
Code:
When an individual file contains several sequence entries, they will be concatenated and the whole concatenated sequence will be aligned to the sequences in the other files.
However if I do the same alignment using the GUI version of Mauve there is the distinction among contigs in each genome when visualizing the final alignment, which makes me think that somehow that information is stored somewhere inside some other file that not the .xmfa.
Do you know where or how could I cross data among the output files generated by progressiveMauve in order to extract the regions of a singular contig that were aligned?
Thank you very much in advance.
Best regards,
George Condomitti.