[BioC] Protein/peptide mass

[Thomas Girke]

John,
Allow me to post some comments to your question rather than providing an immediate 
answer.
	
On UNIX-type OSs, like Linux or MacOSX, I usually run EMBOSS 
command-line programs directly from R using the systems("myemboss_program") 
command and slurp the results into R data frames with its standard data import 
functions (e.g. read.table, read.Lines). The import step often requires some knowledge 
about R's regular expression utilities for reformatting the results as needed. 
Knowledge about BioPerl is often very helpful as well. The advantage of this 
approach is that one can post-analyze and plot almost any type of bio- or 
drug-informatics program in R. However, to do this one needs to have some 
basic knowledge of R, mostly for the import step of very variable data structures. 

For the future it would be very useful to have some BioC utilities that will allow
a more user-friendly data import from EMBOSS, BLAST and hundreds of other 
non-R-based bioinformatics programs.

I would be interested to know whether members on this list are working on packages 
that will facilitate this integration with external sequence analysis tools? 

Thomas


On Wed 05/24/06 16:31, john seers (IFR) wrote:
> Hello All
>  
> Apologies in advance if this is an obvious question but I have searched
> and cannot find an answer or a straightforward way to do it. 
>  
> Is there a way to calculate the mass of a protein/peptide using
> R/Bioconductor?  i.e. like the Expasy "PeptideMass" web page or like the
> EMBOSS pepstats? 
>  
> Regards
>  
> John Seers
>  
>  
>  
>  
>  
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> 
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-- 
Thomas Girke, Ph.D.
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