[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 10, Issue 20
Chris Upton
cupton at uvic.ca
Wed Aug 31 12:16:39 EDT 2005
Hi,
We could probably modify our Base-By-Base program to do that if you
want.
See www.virology.ca under workbench.
Do you just need an editor or something to do the alignment?
Chris
Chris Upton Ph.D. Associate Professor
Biochemistry and Microbiology Tel. 250-721-6507
University of Victoria Fax 250-721-8855
P.O. Box 3055 STN CSC
Victoria, BC V8W 3P6
Canada
web.uvic.ca/~cupton
www.virology.ca
www.sarsresearch.ca
On Aug 31, 2005, at 9:04 AM, bio_bulletin_board-
request at bioinformatics.org wrote:
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> Today's Topics:
>
> 1. aligning character data other than DNA or protein
> (Corn? HW Klaassen)
> 2. Re: aligning character data other than DNA or protein
> (Iain Wallace)
> 3. Re: aligning character data other than DNA or protein
> (Corn? HW Klaassen)
> 4. Re: aligning character data other than DNA or protein
> (Gad Abraham)
> 5. Re: aligning character data other than DNA or protein
> (Daniel Lang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 31 Aug 2005 09:04:51 +0200
> From: Corn? HW Klaassen <c.klaassen at cwz.nl>
> Subject: [BiO BB] aligning character data other than DNA or protein
> To: "The general forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
> Message-ID: <43155693.3080706 at cwz.nl>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 31 Aug 2005 09:24:25 +0100
> From: Iain Wallace <iain.m.wallace at gmail.com>
> Subject: Re: [BiO BB] aligning character data other than DNA or
> protein
> To: "The general forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
> Message-ID: <8cff3eb8050831012457cdda37 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>>
>> _______________________________________________
>> Bioinformatics.Org general forum -
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 31 Aug 2005 11:35:34 +0200
> From: Corn? HW Klaassen <c.klaassen at cwz.nl>
> Subject: Re: [BiO BB] aligning character data other than DNA or
> protein
> To: "The general forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
> Message-ID: <431579E6.9070201 at cwz.nl>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>>>
>>> _______________________________________________
>>> Bioinformatics.Org general forum -
>>> BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Bioinformatics.Org general forum -
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>>
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 31 Aug 2005 19:45:20 +1000
> From: Gad Abraham <gabraham at cs.rmit.edu.au>
> Subject: Re: [BiO BB] aligning character data other than DNA or
> protein
> To: "The general forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
> Message-ID: <20050831094520.GA12159 at cs.rmit.edu.au>
> Content-Type: text/plain; charset=unknown-8bit
>
>
>>> 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.?
>>>>
>
> Sorry for breaking the chain, I lost the previous email.
>
> What is your distance measure between the characters? +1 for match and
> -1 for mismatch?
>
> If you know how to program, you can do this in Perl or even C very
> easily (or adapt a script so it accepts arbitrary characters).
>
> Cheers,
> Gad
>
> --
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> gabraham at cs.rmit.edu.au
> http://yallara.cs.rmit.edu.au/~gabraham
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 31 Aug 2005 13:02:58 +0200
> From: Daniel Lang <daniel.lang at biologie.uni-freiburg.de>
> Subject: Re: [BiO BB] aligning character data other than DNA or
> protein
> To: "The general forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
> Message-ID: <43158E62.1040504 at biologie.uni-freiburg.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>>>>
>>>> _______________________________________________
>>>> Bioinformatics.Org general forum -
>>>> BiO_Bulletin_Board at bioinformatics.org
>>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioinformatics.Org general forum -
>>> BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Bioinformatics.Org general forum -
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>
> --
>
> 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.
> #################################################
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Bioinformatics.Org general forum -
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
> End of BiO_Bulletin_Board Digest, Vol 10, Issue 20
> **************************************************
>
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