[Mauve-users] mauve viewer

[Esakimuthu P. N. P. <ni...@im...>]

Dear All,



I am using Mauve (progressive Mauve) to align whole genomes of two closely related genomes (grasscarp and zebrafish) and the objective is to determine the extent inter and intra-chromosomal rearrangements.



For this comparison, a seed weight of 19 and LCB weight of 2000 was used.  The resulting .XMFA alignment file was uploaded in the Mauve viewer. I am able to visualise the rearrangements between these two genomes.



However I couldn't see any representation for the "inter-chromosomal boundaries" i.e. a line that demarcates the neighbouring chromosomes in the reference genome. From the Mauve viewer, View--> Styles, the option for Chromosome/contig boundaries is turned on. Still, unable to see any lines that demarcate the chromosome boundaries (except the beginning and end of the whole genome). The sequences of all chromosomes are concatenated and the coordinates of the concatenated chromsomes are shown, without any marking demarcating the chromosomes.



I have attached a snapshot of the view (have turned off the LCB connecting lines for this snapshot). Can you kindly advise if there a way to visualise the boundary lines for each chromosome?. Also appreciate if you can comment on the suitability of the parameters (see weight and LCB weight) used by me for aligning these two genomes.



Thank you,
Kind regards,
Nisha


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