[EMBOSS] non-overlapping matches in fuzznuc?
pmr at ebi.ac.uk
Thu Oct 13 08:44:33 UTC 2011
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!
More information about the EMBOSS