[R] Package for Molecular Properties

[David Winsemius]

> On May 3, 2018, at 12:58 AM, Spencer Graves <spencer.graves using effectivedefense.org> wrote:
> 
> 
> library(sos)
> 
> 
> (mp <- findFn('{molecular properties}'))
> 
> 
>       ** found 7 matches in 4 packages and opened two web pages in my default browser with (a) the 7 matches and (b) the 4 packages. The first function was something for amino acids, like you suggested.  Two others returned compound and substance information from PubChem.
> 
> 
>       Does this help?
>       Spencer
> 
> 
> On 2018-05-02 19:17, bbb_aaa using verizon.net wrote:
>> All
>> 
>> Is there a package or library that will, given a nucleotide sequence
>> 
>> 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law)
>> 2. calculate molecular weight
>> 3. return it's complementary sequence

I second Spencer Graves suggestion if using sos::findFn. I use that function on a daily basis and find it very useful.

For #3 I suspect that you would need to specify whether you are dealing with RNA or DNA since the term complementary would have different implementations. Once that is done you could get a 5' sequence from a 3' sequence input by a simple use of base function `chartr`. Assuming the nucleotides were limited to CGTA (DNA) then:

> set.seed(123)
> seq <- sample( c("C","G","T","A") , 10, repl=TRUE)
> seq=paste0(seq,collapse="")
> seq
[1] "GAGAACTATG"
> chartr( old="CGTA", new="GCAT", seq)
[1] "CTCTTGATAC"

Caveat: I'm not a biologist, nor have I ever really done biochemistry. This was from memory of decades-old biology course. Check all the assumptions and assertions with a domain expert.

>> 
>> I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids.
>> 
>> Any pointers, etc. would be great.
--

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law