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.
> ------------------------------------------------------------------
> ------------
> 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
--
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.
------------------------------------------------------------------------------
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
