mauve-users

[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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Re: [Mauve-users] mauve viewer

[Aaron D. <aar...@ut...>]

Hi Nisha,
I notice in your screenshot that the genomes are labeled with "(no
annotations loaded)".
That means the viewer was unable to find and read the original sequence
file that was aligned.
This can happen if the files are moved around from their location after
alignment, especially if the full path name to the sequence file was
given during alignment.
Without reading the original sequence files, the viewer has no way of
knowing where the assembly contig (or chromosome in the case of fully
scaffolded chromosome assembly) boundaries are located, and therefore
can not show the vertical red bars at the boundaries.
There are at least two ways to solve the problem. One would be to
recompute the alignment with just the sequence file name (not full
path) and keep the output in the same directory, and if the files must
move, move these all together. Another approach would be to do a search
& replace in your existing alignment file to provide the correct file
paths to the two fasta files.
One comment about your objective: some of the fish lineages have
undergone whole genome duplication. progressiveMauve will only align
what its scoring function identifies as the contextually conserved copy
of a repeat, and in the case where one of the genomes has undergone a
WGD event the copy to align becomes ambiguous. It could be either copy
that gets aligned, or neither! So I suggest interpreting any results
from progressiveMauve with extreme caution if you are analysing
rearrangement rates in the presence of WGD.
-Aaron
On Mon, 2017-04-10 at 02:44 +0000, Esakimuthu Pillai Nisha PILLAI
wrote:
> 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, Viewà 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.
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-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman





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