[Bioperl-l] error during installation

Du, Peng du at ibio.jp
Tue Jun 19 11:25:42 EDT 2012


As to the Clustalw problem, it turned out that, I didn't install it in
the first place, I am very sorry for the stupid mistake. It is alright
now. But, as to dpAlign, I compared the alignment of non coding
regions of two species with dpAlign (in an Intel x86 but much slower
machine where dpAlign is good) and Clustalw respectively and checked
the output, I found that, each with default parameters, the alignments
by dpAlign were better than that by Clustalw, and there was a
tremendous difference in the outputs in terms of A<=>G, C<=>T, AG<=>CT
substitutional rate and divergence by Tamura-Nei Model between the two
alignments. The values are much smaller with dpAlign.  Since I am a
newbie, I don't quite understand why there was such a difference. Is
it might because of the Clustalw is designed for multiple alignment or
the default parameters are not appropriate?

I am now investigating other tools available in the main distribution
of  BioPerl, but I have no idea whether there is a good substitution
of dpAlign in context of non coding region alignment.

Thank you very much.

On Tue, Jun 19, 2012 at 11:14 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> This seems specifically like a clustalw problem (the error code is a giveaway).  What version of clustalw is this?  It should run with more recent versions.
>
> Re: dpalign, is there something that module specifically does that other tools can't provide?   If it proves useful I would rather move it and all related tools into it's own distribution for separate release (so any bugs can be fixed more readily w/o relying on core changes).
>
> chris
>
> On Jun 17, 2012, at 6:16 AM, Du, Peng wrote:
>
>> Sorry for that, actually I am using it, but I forgot to paste the code
>> in which I invoked "pairwise_alignment" with dpAlign.
>> At the same time, I met another problem regarding "ClustalW". The
>> error message was"MSG ClustalW call align crashed -1". It might be
>> because of incorrect installation of BioPerl-run. But, I didn't
>> encounter any error message while installing it.
>>
>> Thank all of you.
>>
>> Peng
>>
>> On Sun, Jun 17, 2012 at 8:01 PM, Leon Timmermans
>> <l.m.timmermans at students.uu.nl> wrote:
>>> On Sun, Jun 17, 2012 at 7:37 AM, Du, Peng <du at ibio.jp> wrote:
>>>> At present, I want to use dpAlign, I don't know I still need bio-ext
>>>> to perform dpAlign or I could modify my code to achieve this without
>>>> bio-ext package.
>>>> Thank you.
>>>
>>> Bio::Tools::dpAlign is in the main BioPerl distribution, as can be
>>> seen here: https://metacpan.org/module/Bio::Tools::dpAlign. You will
>>> need to take out that «use Bio::Ext::Align;», but you don't seem to be
>>> using it anyway.
>>>
>>> Leon
>>
>>
>>
>> --
>>
>> Peng Du
>> Graduate School of Information Science and Technology, Hokkaido University
>> Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
>> Email: du at ibio.jp Tel: +81 80 3268 9713
>



-- 

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713



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