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?
Cheers
Aengus
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
EMBOSS Team
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