Re: [MUMmer-help] whole genome alignment question

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

You are reading that correctly. With default options, Nucmer's sensitivity
is tuned for alignments >90% identity. Your genomes are likely too
divergent to align well w/ these parameters. If they are small bacterial
genomes you could try something like:

nucmer -maxmatch -l 18 -c 50 -g 200

To improve sensitivity, but in general the tool is not well suited for
sensitive alignments.

-Adam


On Tue, Mar 3, 2015 at 11:31 AM, Diogo Camacho <dio...@gm...
> wrote:

> A follow up to my earlier question:  when I looked at the output from
> dnadiff (the .report file) I saw this:
>
> [Bases]
> TotalBases                   1837281              2427048
> AlignedBases            47871(2.61%)         47261(1.95%)
> UnalignedBases       1789410(97.39%)      2379787(98.05%)
>
> [Alignments]
> 1-to-1                            28                   28
> TotalLength                    23369                23403
> AvgLength                     834.61               835.82
> AvgIdentity                    83.96                83.96
>
> M-to-M                            67                   67
> TotalLength                    86329                86650
> AvgLength                    1288.49              1293.28
> AvgIdentity                    87.96                87.96
>
>
> Does this output mean that I’m only really aligning the query genome to
> roughly 3% of my reference genome, and that alignment has an average
> identity of 80%+?   Or am I reading this wrong?
>
> Thanks!
>
>
>
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
>
>
>
>
>
> > On Mar 3, 2015, at 10:30 AM, Adam Phillippy <aph...@gm...>
> wrote:
> >
> > Hi Diogo,
> > If you run the 'dnadiff' script that comes with MUMmer it will generate
> a .report file that will include global similarity metrics based on Nucmer
> alignments.
> >
> > Best,
> > -Adam
> >
> >
> > On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <
> dio...@gm...> wrote:
> > Hi,
> >
> > This is a very naive, simple question, but I can’t seem to locate a good
> answer for it on the manual.  I have a set of bacterial genomes that I want
> to align against a different (single) bacterial genome.  The obvious tool
> to do this seems to be NUCmer and I did a test run of 1 genome against the
> “reference” genome by doing:
> >
> > nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE
> COMPARED>
> >
> > NUCmer runs fine and when I do show-coords I get the table with the
> alignments and the respective identity between the 2 genomes I am
> comparing.  But what I would like would be to get a single, global, percent
> identity score between the 2 genomes, as I basically want to compare the
> two genomes at a global level.  Is there a simple way to do this using the
> MUMer suite?
> >
> > Many thanks!
> >
> >
> > Best,
> > d.
> >
> >
> >
> > ----------
> > Diogo Camacho
> > e: dio...@gm...
> > p: (617) 945-4383
> >
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> > by Intel and developed in partnership with Slashdot Media, is your hub
> for all
> > things parallel software development, from weekly thought leadership
> blogs to
> > news, videos, case studies, tutorials and more. Take a look and join the
> > conversation now. http://goparallel.sourceforge.net/
> > _______________________________________________
> > MUMmer-help mailing list
> > MUM...@li...
> > https://lists.sourceforge.net/lists/listinfo/mummer-help
> >
>
>