[BiO BB] aligning character data other than DNA or protein

[Felipe Albrecht]

Why you dont use a simple dynamic programming algorithm?



2005/8/31, Daniel Lang <daniel.lang at biologie.uni-freiburg.de>:
> Hi,
> Are you sure, wether it is really Clustal that restricts to 24 chars or
> simply the underlying substitutiion matrix. If this is the case, this
> could be accomplished by writing your own matrix.
> Or you try other tools in combination with adapted substitution matrix...
> Daniel
> 
> Corné HW Klaassen wrote:
> > Iain
> >
> > Clustal only accepts 24 letters. Numbers and other characters are
> > disregarded. So what if I have more than 24 different characters?
> >
> > Corné
> >
> > -----------------------------------------------------------------------------------------
> >
> > dr. Corné H.W. Klaassen, Molecular Biologist
> > Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70
> > Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands.
> >
> > tel: #31-24-3658670 (office)
> > tel: #31-24-3658677 (direct)
> > fax: #31-24-3658671
> > E-Mail: c.klaassen at cwz.nl
> >
> >
> >
> > Iain Wallace wrote:
> >
> >> Hi,
> >>
> >> I think ClustalW can do that, as long as it is in a sequence format.
> >>
> >> Iain
> >> On 8/31/05, Corné HW Klaassen <c.klaassen at cwz.nl> wrote:
> >>
> >>
> >>> Hi all,
> >>>
> >>> Does anybody know of a convenient tool to align stretches of character
> >>> data other than DNA or protein (i.e. numbers: 01-02-03-05 and
> >>> 01-02-04-05) that is also able to deal with insertions and deletions
> >>> etc.?
> >>>
> >>> Thanks,
> >>>
> >>> Corné
> >>>
> >>> --
> >>> -----------------------------------------------------------------------------------------
> >>>
> >>> dr. Corné H.W. Klaassen, Molecular Biologist
> >>> Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70
> >>> Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands.
> >>>
> >>> tel: #31-24-3658670 (office)
> >>> tel: #31-24-3658677 (direct)
> >>> fax: #31-24-3658671
> >>> E-Mail: c.klaassen at cwz.nl
> >>>
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> >>>
> >>
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> --
> 
> Daniel Lang
> University of Freiburg, Plant Biotechnology
> Schaenzlestr. 1, D-79104 Freiburg
> fax: +49 761 203 6945
> phone: +49 761 203 6974
> homepage:  http://www.plant-biotech.net/
> e-mail: daniel.lang at biologie.uni-freiburg.de
> 
> #################################################
> My software never has bugs.
> It just develops random features.
> #################################################
> 
> 
> 
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