[Biojava-l] SVDSuperimposer

[Raphael André Bauer]

On Fri, May 8, 2009 at 7:37 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Raphael,
>
> Thanks for posting the link to "LaJolla" (funny that you chose this
> name, it is the part of the town where my university is located...).
> This is very interesting and exactly the kind of applications we are
> happy to see BioJava being used for.
Well. Phil Bourne and the PDB are there (and I think you are also
somehow connected to both)... I also heard that LaJolla might have
nice beaches, sunny weather and the surf?... So LaJolla definitely is
a good name for a boring structural RNA and protein alignment
algorithm...
>
> Do you want to provide a link back to your project site at
> http://biojava.org/wiki/BioJava:BioJavaInside and also add your paper
> to the list of papers that are using BioJava?
done
>
> About the  BioJava algorithm : If you have an example where the
> BioJava structure comparison does not give the result you would
> expect, could you send it to me so I can take a look ?
I did not write down the examples (I thought, that the protein
alignment of BioJava is somehow alpha because of "personal
communication of..."). But the examples where simple. If I rediscover
them I will  let you know.

Maybe it is also of help to mention in the source code or on the
webpage of the cookbook: "If our protein alignment alg delivers
strange results please let us now..." or so.. So that users are aware
of submitting strange results...


Thanks,

Raphael

>
> Thanks,
> Andreas
>
>
> On Fri, May 8, 2009 at 6:13 AM, Raphael André Bauer
> <raphael.andre.bauer at gmail.com> wrote:
>> 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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