[Biojava-l] SVDSuperimposer

[Raphael André Bauer]

On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michal,
>
> The SVD superimposer actually does the same Singular Value
> Decomposition in both BioJava and BioPython. The difference is that
> BioJava also contains a complete alignment algorithm that can
> calculate a structure alignment, if the region of similarity between 2
> proteins is not known a priori.
>
> See also here:
> http://biojava.org/wiki/BioJava:CookBook:PDB:align  and
> http://biojava.org/wiki/BioJava:CookBook:PDB:aboutalign

Maybe it is interesting for you to know that we developed a generic
algorithm for the structural alignment of RNA and proteins called
"LaJolla". The reference implementation is built using BioJava and
released as open source at http://lajolla.sourceforge.net. I think
LaJolla is straight forward to use and modify if you know how to use
Maven and the BioJava core classes.

Btw. The algorithm for the alignment of proteins used by BioJava
yielded sometimes strange results - but I did not do an exhaustive
evaluation. But maybe LaJolla is an alternative in those cases.

Additionally -- if the BioJava project is interested in integrating
LaJolla into BioJava this is really not a problem -- but I do not know
if it blurs the clean toolkit/library character of BioJava.

We are open for all suggestions regarding the algorithm and also
regarding a cooperation with BioJava...

Thanks,

Raphael
@Michal: LaJolla is also partly made in Poland -- so mabye you some
people by chance..

>
> Andreas
>
> On Thu, May 7, 2009 at 5:24 AM, Michal Lorenc <m.t.lorenc at wp.pl> wrote:
>> Hello Andreas,
>> SVDSuperimposer from BioPython works only with proteins which have the same
>> length, but in BioJava it does not matter.
>>
>> Do you published how SVDSuperimposer in BioJava works or do you know where
>> could I found more information?
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>> Michal
>>
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