[Biojava-l] Calculating edit distance between 2 DNA Sequences

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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
> <biojava at hannes.oib.com> 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
>> <biojava at hannes.oib.com> 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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