Re: Isoelectric point and molecular weight calculations with BioJava
George Waldon <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hello Peter & Andreas I effectively did some work on these methods, mostly fixing and adding the ExPASy algorithm that was kindly provided to me. I think it makes a lot of sense to port all physico-chemical property calculations related to amino acids and polypeptides to bj3, as suggested by Andreas, and I definitively support the effort. We could smoothly deprecate the bj1 package when this is done. Let me know how I could help. Thanks George Quoting Peter Troshin <[email protected]>: > Hi Andreas, > > In fact I'd be happy to help with the development of the tools for > simple physico-chemical properties calculation for peptides. We > could port George’s code (assuming he is happy with this) from > BioJava 1.8 but we can also provide a few other methods. A couple of > projects in the lab where I work would have benefited from having > these calculations readily available. > > I was thinking about participation in the Google Summer of Code > (GoSC) this year as a mentor, and I think this would be an easy > project for a student. What do you think about this? > > Thank you for your prompt reply. > > Regards, > Peter > > > > On 24/02/2011 16:54, Andreas Prlic wrote: >> Hi Peter, >> >> if you get a copy of biojava 1.8, it is still there. However I would >> like to port this to biojava 3 as well.. George do you want to help me >> with that, since you are one of the authors of this package? The basic >> support for chemistry in BioJava 3 is a bit better... (e.g. Element >> class) >> >> Andreas >> >> On Thu, Feb 24, 2011 at 7:33 AM, Peter >> Troshin<[email protected]> wrote: >>> Hi, >>> >>> I've noticed that BioJava up to about version 1.7 had an >>> org.biojava.bio.proteomics package, which had methods for isoelectric point >>> and molecular weight calculations for peptides. I could not find this >>> package in the BioJava 3.0.1 API. I’d like to use these methods and wonder >>> if there are any equivalent methods available in the latest version of >>> BioJava? >>> >>> Thank you for your help, >>> >>> Kind regards, >>> Peter >>> >>> Dr Peter Troshin >>> Bioinformatics Software Developer >>> Phone: +44 (0)1382 388589 >>> Fax: +44 (0)1382 385764 >>> The Barton Group >>> College of Life Sciences >>> Medical Sciences Institute >>> University of Dundee >>> Dundee >>> DD1 5EH >>> UK >>> >>> >>> >>> _______________________________________________ >>> 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