Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Export of RNA presets to IDT notation (standard IDT monomers) #1654

Closed
olganaz opened this issue Jan 31, 2024 · 1 comment · Fixed by #1908
Closed

Export of RNA presets to IDT notation (standard IDT monomers) #1654

olganaz opened this issue Jan 31, 2024 · 1 comment · Fixed by #1908

Comments

@olganaz
Copy link
Collaborator

olganaz commented Jan 31, 2024

Background
Users may need to generate IDT notation for modified RNA to be able to order this kind of molecules through IDT web site.
This task dedicated to the export of presets with defined subunits.

Requirements
There could be four types of IDT monomers for export:

  1. Standard monomers - nucleotides, which could be exported as [s]<Base>[*]
    where:
    Base - standard unmodified nucleotide base symbol (see table below)
    s - optional symbol of the sugar that makes the nucleotide (see table below). If not specified, standard sugar deoxy-ribose (dR) is implied.
    * - optional indicator of modified phosphate. If specified, indicates that Phosphorothioate (sP) is included into nucleotide, otherwise standard phosphate (P) is implied.
    The last nucleotide is considered to lack phosphate, so * couldn't be the last symbol in the sequence.

Examples
TBD

@olganaz olganaz changed the title Export modified RNA to IDT format Export of standard IDT monomers Apr 3, 2024
@olganaz olganaz changed the title Export of standard IDT monomers Export of RNA presets to IDT notation (standard IDT monomers) Apr 3, 2024
@olganaz olganaz added this to Product Backlog in Indigo via automation Apr 3, 2024
@AliaksandrDziarkach AliaksandrDziarkach added this to the Indigo-1.20.0-rc.1 milestone Apr 9, 2024
@AliaksandrDziarkach AliaksandrDziarkach self-assigned this Apr 9, 2024
AliaksandrDziarkach added a commit that referenced this issue Apr 11, 2024
AliaksandrDziarkach added a commit that referenced this issue Apr 12, 2024
…1908)

Co-authored-by: Aliakasndr Dziarkach <Aliakasndr.Dziarkach@gmail.com>
Indigo automation moved this from Product Backlog to Done Apr 12, 2024
@AlexeyGirin
Copy link
Collaborator

Will be tested in the context of epam/ketcher#4495

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Indigo
  
Done
Development

Successfully merging a pull request may close this issue.

4 participants