[BioC] Protein/peptide mass

[john seers (IFR)]

Hi Thomas

Thank you very much for your reply.

There are some functions in the packages "seqinr" and "Biostrings", in
fact quite a lot, but not one to calculate the mass of a peptide that I
can find. So I was being forced down the route of having to call an
EMBOSS program and parse the results. The problem with that is the
interface is not easy - often needs a file as input in some standard
format - not just passing in a string on the command line.

The other way I thought might be possible was to use the online
facilities of something like Expasy's "PeptideMass" but I cannot get
that to work. Does anybody have any idea if that is possible?

Regards

John Seers





 
---

John Seers
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-----Original Message-----
From: Thomas Girke [mailto:thomas.girke at ucr.edu] 
Sent: 24 May 2006 18:35
To: john seers (IFR)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Protein/peptide mass


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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