[EMBOSS] non-overlapping matches in fuzznuc?

Aengus Stewart aengus.stewart at cancer.org.uk
Thu Oct 13 09:31:56 UTC 2011

So Peter is right about what I want returned - the best match, but of course has pointed out the problem with having 2 best matches for the same region ( in this example 104-113, 105-114).  However, it is still the case that the "real" result is 4 hits rather than 9.

I dont know if my example is a special case or not so it would be good as Peter suggests if someone else has used fuzznuc in a similar way.  Though surely if you include any mismatch at all for your pattern search then you automatically have this scenario of returning multiple results for the same location?


On 13/10/11 09:44, Peter Rice wrote:
> On 13/10/2011 08:45, Jon Ison wrote:
>> Hi chaps (Aengus !)
>> If I understood Aengus' msg. what's needed is something that simply combines overlapping hits (for
>> a given pattern) into one or more non-overlapping "region of hits", and reports those regions e.g.
>>      Start     End  Strand Pattern_name Mismatch Sequence
>>         54      65       + pattern1            5 GCCAAATAAGGG
>>        104     115       + pattern1            5 CCTAAATAAGGG
>>        179     188       + pattern1            2 CCTTGCTTGG
>>        190     200       + pattern1            6 CCGATTAGAGC
>> Mismatch in this case is reporting the sum of mismatches from before.  A column for number of
>> (sub)matches would also be needed.  Is that right Aengus?
> I'm not sure that adding the mismatches is sound. I'd assume just a best
> hit from the overlapping matches.
>> The above might give a useful result depending in the input pattern.  It would I think be easy
>> enough to implement.
> This is a report output, so post-processing could be done by trimming
> the results before output using an associated qualifier.
> Still not sure how useful it would be, we need more feedback from other
> users on this one please!
> Peter Rice
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Aengus Stewart                                 Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
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