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When I do:

SequenceAlignment["-0.999995756767227832383453368554576431549","-0.999995756767227832383346049698547342279"]

I get:

{-0.99999575676722783238,{,3},34,{533,6049},6,{,9},8,{5,},54,{5,},7,{6,3},4,{3154,227},9}

Clearly there is an extra 3 that is missing as a common sequence number at the end:

-0.9999957567672278323834...
-0.9999957567672278323833...

Is this a bug? (Using Mathematica 10.0.2)

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2 Answers 2

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Mathematica took the alignments in the following way

-0.99999575676722783238x34
-0.99999575676722783238334
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3
  • $\begingroup$ Yes, but why this behavior? $\endgroup$
    – Giovanni F.
    Mar 10, 2015 at 14:09
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    $\begingroup$ @Giovanni Well, I haven't checked the details but it's using the Needleman-Wunsch algorithm. $\endgroup$
    – Dr. belisarius
    Mar 10, 2015 at 14:22
  • $\begingroup$ Ok. Thanks. I thought it was an exact method of finding these sequences. $\endgroup$
    – Giovanni F.
    Mar 10, 2015 at 16:48
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If you increase the `GapPenalty" (default is zero) you can pick up the 3; however, the difference sequences get longer and the total similarity score decreases.

SequenceAlignment["-0.999995756767227832383453368554576431549", \
"-0.999995756767227832383346049698547342279", GapPenalty -> 3]

{"-0.999995756767227832383", {"453368554", "346049698"}, "5", {"7643154", "4734227"}, "9"}

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