coding and non-coding region of the viral genome

Question

[G.S]

Hi,

Any idea how to identify the Beginning and end positions of the coding and non-coding region of the viral genome? Is there a dedicated tool to do this?

coding
    start   end
    99  518
    628 1002
    1141    2316
    2347    3072
    3262    4032
    4304    4498
    4689    5585
    5662    7386
    7607    8191
    8160    8432
    8499    14996

Non_coding      
    start.   End
    45          99
    596         628
    1126    1140
    2330    2345
    3253    3261
    4220    4301
    4674    4687
    5649    5661
    7598    7606
    8491    8496

Is this correct?

Many thanks

[dthorbur]

Are there already annotations published for the genome? If so, I doubt there is a dedicated tool since this is a simple task of parsing the coordinates of a GFF/GTF/BED annotations file. Easily done with even a basic grasp of R or Python.

If not, then there are viral genome annotation tools available. Not my field, but a google showed a handful of dedicated viral genome annotation tools are available.

[G.S]

As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ?

I have attached a pic to explain my viral genome . Thanks in advance

[dthorbur]

You also have intronic regions between exons that also count as non-coding regions. Psuedogenes and non-coding RNAs too. I'm sure there are other classes I'm forgetting.

I'm not going to write you code. You need to show initiative and understanding of the file types and what information is available. Have a go at writing a script yourself, and if you're stuck, show us what you've done and we'll be more willing to help. "Do my work for me" requests don't go down well on forums.

[G.S]

Thanks for the explanation.

I have already provided a code in a previous post.

virus genome annotation

In this post, my concern was about understanding how how to annotate my genome correctly?

[dthorbur]

I think you need to learn how to write a loop or a function that would parse the annotations file, and extract the coordinates rather than hard coding each and every entry as this would take you a very long time and is prone to mistakes.

The logic is simple - add start and end coordinates of a given entry to a new data table, and in another column add an if/else statement to add whether this entry is coding or not.