Re: [MUMmer-help] overlapping matches when calling mummer -mum

[Adam P. <aph...@gm...>]

Hi Afif,
This is the intended behavior of the program. I believe you are
misinterpreting the meaning of a maximal unique match. A maximal match is
defined as a match that cannot be extended on either end without
encountering a mismatch. Just because a MUM contains a repetitive sequence,
does not make the whole MUM non-unique. For the two sequences with unique
seqs 'U' and tandem repeats 'T':

A: UUUTTTUUU
B: UUUTTUUU

There would be MUMs found on either side: UUUTT and TTUUU. These two MUMs
overlap on both T's in B and overlap on the middle T in A. Both MUMs are
unique, i.e. they don't appear anywhere else as a whole ... though they do
contain substrings that are repetitive. I hope this little example makes it
a little more clear.

Nucmer or dnadiff are the best tools in MUMmer for comparing contigs to a
reference. I prefer to run:
> nucmer -maxmatch -banded ref.fna. contigs.fna
> delta-filter -q out.delta > out.qdelta
> show-coords -THrcl out.qdelta > out.coords

This will report the best alignments found for each contig to the
reference, which you can parse to identify large differences or run
show-snps to identify smaller polymorphisms.

Best,
-Adam


On Mon, Nov 2, 2015 at 2:54 PM, Afif Elghraoui <ael...@sd...> wrote:

> Hello,
> I am trying to get a very basic comparison between a de novo assembled
> microbial genome and a reference sequence. I used nucmer at first, but
> there was a tandem duplication that was causing overlapping alignments
> and I just wanted to know precisely what was different. It appears that
> the plain mummer program would be appropriate for finding this out, so I
> called mummer as follows:
>
> mummer -mum <reference> <query>
>
> By using the -mum flag, I thought that I'm not supposed to be seeing any
> overlap in the matches in both the query and reference, but I found an
> instance of this in those positions where I was previously getting
> overlaps in my nucmer alignments:
>
> 3569553   3570622    132349
> 3701734   3702919     39749
>
> If I understood the format of the output correctly, the first match here
> overlaps the second in the reference (3569553+132349 = 3701902 >
> 3701734) and the query. By manual inspection of blast results of these
> positions, I know that there is a tandem repeat in this region where the
> query has five copies and the reference has three copies and the overlap
> in the matches here matches all three copies in the reference twice and
> also matches one of the copies in the query twice.
>
> This doesn't look to me like intended behavior of the program,
> especially since I'm not using -maxmatch. Am I doing something wrong or
> misunderstanding anything here? I'm using MUMmer 3.23 as packaged in
> Debian 8. I can provide my query genome privately if necessary.
>
> Many thanks and regards
> Afif
>
> --
> Afif Elghraoui
> Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
> San Diego State University
> Alvarado Medical Center
> 6367 Alvarado Court, Suite 206
> San Diego, CA 92120
> p. 858-222-0454
> http://tuberculosis.sdsu.edu
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>