Re: [MUMmer-help] nucmer and repeats

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

Hi Alesk,
You are probably correct about the overlapping sequences. Nucmer is meant
for finding large regions of similarity and uses some heuristics to speed up
the search, as such it is not well suited for exhaustively finding all short
matches.

Since you are looking for exact 20 bp matches, you can use 'mummer'

> mummer -b -c -l 20 -maxmatch my.ref my.qry > my.out

This will identify all 20 bp (and longer) exact matches between your
reference and query.

Best,
Adam Phillippy


On Jan 30, 2008 6:07 AM, alesk sboob <ale...@ya...> wrote:

>
> Hi all,
>
> I use MUMmer since few days, it's really a great and fast alignment tools,
> thanks to developers!
>
> However, i tried to find perfect match for ~20 nucleotids sequences on a
> chromosome. I used nucmer with the following command line :
> nucmer -maxmatch -d 0 -c 0 -l 20 --coords --nooptimize --nosimplify
> refSequence.fa QuerySequences.fa
>
> I compared the nucmer exact matches results with blast exact matches
> results on the same sequences. Unfortunately nucmer failed to find some
> exacts matches for several sequences.
>
> I looked at these sequences and matchs found by nucmer and blast. Here his
> a part of the reference sequence and a query sequence for with all matches
> where not founded with nucmer.
> >PartOfReference
> GAGAGAGAAAGAGAGAAAGAGAGAAAGAGAGAAAGAGAGAAAGAGAGAAAGAGAGAAAGAGAGAG
>
> >MyQuerySequence
> AGAAAGAGAGAAAGAGAGAAAGA
>
>
> As u can see, these 2 sequences got the same repeat motif. I think that
> nucmer failed to find all matches cause they are overlapping each other.
> Did i make a mistake in my command line? Anyone got a solution?
>
> Best,
>     alesk
>
>
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