R help - May 2018 - Package for Molecular Properties

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 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.

thank you in advance
Indr

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 at 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 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.
>
> thank you in advance
> Indr
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

... In addition, you may wish to also post on the Bioconductor list
for this sort of thing.

-- Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, May 3, 2018 at 12:58 AM, Spencer Graves
<spencer.graves at 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 at 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 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.
>>
>> thank you in advance
>> Indr
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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