Hi Hannes,
You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
But it will not stop when a maximal number of errors is reached ...
JS
Le 7 nov. 2011 à 15:42, Andreas Prlic a écrit :
> Hi Hannes,
>
> you are right, this does not exist yet. Somebody else asked the same
> question a few weeks ago. As such it would be great if you could
> provide a patch, there might be other people interested in that, too.
>
> Andreas
>
> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandstätter-Müller
> <[email protected]> wrote:
>> Following up:
>>
>> If there is no such thing, should I make it available if I write it?
>>
>> Hannes
>>
>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandstätter-Müller
>> <[email protected]> wrote:
>>> Hi!
>>>
>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>> distance between two sequences? I could not find anything in the docs
>>> at first search.
>>>
>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>> insertions, deletions, and substitutions. Ideally, there would be an
>>> option to abort the comparison if the number of mismatches exceeds a
>>> certain number.
>>>
>>> Hannes
>>>
>>
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>>
>
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