Re: [MUMmer-help] whole genome alignment question

[Diogo C. <dio...@gm...>]

That’s what I thought.  I aligned my reference to a very similar (same genus, same species, different strain bacterium) and I got a very high similarity and a very high percentage of aligned bases.  Thanks for the tip on nucmer.  I’ll explore that some more to fit my needs.


----------
Diogo Camacho
e: dio...@gm...
p: (617) 945-4383





> On Mar 3, 2015, at 11:48 AM, Adam Phillippy <aph...@gm...> wrote:
> 
> 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
> >
> >
> >
> >
> >
> >
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