On Fri, May 8, 2009 at 7:37 PM, Andreas Prlic <[email protected]> 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 > <[email protected]> wrote: >> On Thu, May 7, 2009 at 2:59 PM, Andreas Prlic <[email protected]> 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 <[email protected]> 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 >>>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
