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
Note: This message may contain confidential information. If this Email/Fax has
been sent to you by mistake, please notify the sender and delete it
immediately. Thank you.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
