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
