[EMBOSS] non-overlapping matches in fuzznuc?

Aengus Stewart aengus.stewart at cancer.org.uk
Wed Oct 12 15:50:36 UTC 2011

Hi Folks,

I couldnt see a command line option to do what I wanted ie return non-overlapping hits.

This is best explained with some sample output.

# Sequence: chr1_174353258_174354335     from: 1   to: 200
# HitCount: 9
# Pattern_name Mismatch Pattern
# pattern1            3 CC[AT](6)GG
# Complement: No

   Start     End  Strand Pattern_name Mismatch Sequence
      54      63       + pattern1            3 GCCAAATAAG
      55      64       + pattern1            . CCAAATAAGG
      56      65       + pattern1            2 CAAATAAGGG
     104     113       + pattern1            1 CCTAAATAAG
     105     114       + pattern1            1 CTAAATAAGG
     106     115       + pattern1            3 TAAATAAGGG
     179     188       + pattern1            2 CCTTGCTTGG
     190     199       + pattern1            3 CCGATTAGAG
     191     200       + pattern1            3 CGATTAGAGC

As you can see this is actually only 4 hits rather than the 9 reported.

I can do this myself with another script but I was wondering if it could be an option?


Aengus Stewart                                 Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
Lincoln's Inn Fields, Holborn, London, WC2A 3LY, UK

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