[Bioperl-l] error during installation

Fields, Christopher J cjfields at illinois.edu
Tue Jun 19 13:38:04 EDT 2012

On Jun 19, 2012, at 12:21 PM, Leon Timmermans wrote:

> On Tue, Jun 19, 2012 at 5:25 PM, Du, Peng <du at ibio.jp> wrote:
>> 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.
> ClustalW uses a heuristic algorithm, it cannot produce a solution that
> is guaranteed to be optimal. dpAlign uses the Miller-Myers algorithm
> (a variant on Needleman-Wunch), that does make such guarantees. It
> should be slower but may produce a better alignment.
> Leon

Agreed.  I think it would be worth pulling this out and releasing it on it's own, maybe including Bio::Tools::dpAlign with it as well.  The key problem is one of maintenance; this code was pretty much written by one developer.  I'll see if I can track Yee Man (the developer) down.


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