GithubHelp home page GithubHelp logo

How to handle plasmids? about ctgap HOT 5 OPEN

ammaraziz avatar ammaraziz commented on August 20, 2024
How to handle plasmids?

from ctgap.

Comments (5)

gokeson avatar gokeson commented on August 20, 2024

Brilliant question.
Most people tend to exclude the plasmid from the phylogeny tree.
We can be smart and have two trees: one for the plasmid to show plasmid evolution and the other for the chromosome.

from ctgap.

ammaraziz avatar ammaraziz commented on August 20, 2024

We'll need a way to separate the plasmid sequence from the core genome of Ct.

Not sure how to handle this in the pipeline at this moment. There's a few options:

  1. Annotate everything, then parse out the contigs annotated with plasmid or similar - not sure how this will go because plasmid annotations could be unpredicatable
  2. blast for dnaA/repA to detect replication gene then pull out
  3. something else?

from ctgap.

gokeson avatar gokeson commented on August 20, 2024

The best way is BLAST and pull.
This is what I do manually anyway.

from ctgap.

ammaraziz avatar ammaraziz commented on August 20, 2024

What blastdb do you use?

from ctgap.

gokeson avatar gokeson commented on August 20, 2024

Sorry, I do my blast in genious without any db of mine.
I can curate a db and send it over tomorrow

from ctgap.

Related Issues (16)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.