[Biojava-dev] BioJava Development

[George Waldon]

Hello Jeff,

First, welcome on this list. Contributions are always welcome and proteins properties is certainly an area where work is needed.

Check the proteomics package org.biojava.bio.proteomics. We already have code to compute molecular masses and isoelectric points. Also consult the file org.biojava.bio.symbol.ResidueProperties.xml. I have added recently the hydropathicity values. There is a pattern for  residue properties involving the class org.biojava.bio.symbol.SymbolPropertyTable (see also ProteinTools).

Please, do not hesitate to ask advice on this list. Personally, I think it is important to give a precise literature reference when biological constants and methods are used.

- George

 


> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
> bounces at lists.open-bio.org] On Behalf Of Jeff Cope
> Sent: Thursday, November 29, 2007 9:11 AM
> To: biojava-dev at lists.open-bio.org
> Subject: [Biojava-dev] BioJava Development
> 
> Hello all,
> 
> 
> 
>             My name is Jeff Cope, and I am currently an undergraduate
> developer working as a research assistant on project where we are
> calculating some values for various protein sequences like isoelectric
> point, instability index, aromaticity, etc. (found here:
> http://trac.boisestate.edu/protcalc/ for those who are interested).
> 
> 
> 
>             As it stands right now we have implemented an applet client to
> server system to communicate the data because we have had to wrap the
> BioPython library on the server side.  I have not been able to find the
> matching functionality in the BioJava Library, although I recognize that I
> might have missed it somewhere in there.
>