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  • Niraks
    Junior Member
    • Aug 2010
    • 1
    #1

    Blast sequence algorithm

    I've got a question regarding the BLASTn search algorithm that I can't quite grasp. Is it possible for two DNA sequences of length 100 may be >90% identical but have no similarity according to the BLASTn search and if so, how?

    Is it to do with differences in alignment with the HSP or it's threshold values?
    Tags: None
  • krobison
    Senior Member
    • Nov 2007
    • 734
    #2
    If they have that high an identity, I can't see how they wouldn't match for BLASTN even with it set to very high stringency. Are you sure everything is being run correctly and that they are really that similar?

    Comment

    • lh3
      Senior Member
      • Feb 2008
      • 686
      #3
      If the 9 mismatches on a 100bp sequence happen to occur at the 11th, 22nd, 33rd,..., 99th positions, BLAST under the default configuration (11-mer) will miss it as there are no seed hits. This is pretty rare, though.

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