> On May 3, 2018, at 12:58 AM, Spencer Graves
> <spencer.gra...@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_...@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
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