Re: [Biojava-dev] what is the default parameters of

[Andreas Prlic-2]

Hi,

That depends on several things. E.g. on the substitution matrix being
used, also on what you want to align.

Here a site that suggests a combination of substitution matrix and gap
penalties: ( BLOSUM62 matrix  with gap opening penalty of 10 and a gap
extension penalty of 0.5)
http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13

To also advertise some related, but ancient work of myself ;-) see:
at: http://peds.oxfordjournals.org/cgi/content/full/13/8/545

Andreas




http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13

2009/9/29 simpleyrx <simpleyrx@...>:

>
> Dear experts,
>
>
> NeedlemanWunsch's constructive funtion in biojava is as below:
> public NeedlemanWunsch(short?match,
>                       short?replace,
>                       short?insert,
>                       short?delete,
>                       short?gapExtend,
>                       SubstitutionMatrix?subMat)
> I would like to know what are the default values to used NeedlemanWunsch. Such as how select match ,replace,insert,delete,gapExtend or subMat parameters ?
>
>
> --
>
>
> Renxiang Yan
>
>
>
>
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> biojava-dev mailing list
> biojava-dev@...
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>
>

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