Question: Calculate Ribosome Binding Score for ORFs?
0
gravatar for DanielC
3 months ago by
DanielC90
Canada
DanielC90 wrote:

Dear Friends,

I am trying to calculate RBS score for a number of predicted ORFs. I have been researching for a way to do this locally since I have many ORFs. Could you please let me know how this can be done? Thanks for your time.

rbs orf • 188 views
ADD COMMENTlink modified 5 days ago by hauken_heyken40 • written 3 months ago by DanielC90
2
gravatar for hauken_heyken
5 days ago by
hauken_heyken40 wrote:

Here: Python standalone implementation of RBS calculator.

https://github.com/hsalis/Ribosome-Binding-Site-Calculator-v1.0

ADD COMMENTlink written 5 days ago by hauken_heyken40

Thank you for this Hauken!

ADD REPLYlink written 5 days ago by DanielC90
1
gravatar for hauken_heyken
4 weeks ago by
hauken_heyken40 wrote:

When you say RBS score, do you mean procaryote ribosome binding sites calculator using free energy like this, but local version of it ? https://salislab.net/software/predict_rbs_calculator

Or eukaryote Kozak score, as implemented in ORFik ? https://rdrr.io/bioc/ORFik/man/kozakSequenceScore.html

Or Ribo-seq scores like this one in ORFik ? https://rdrr.io/bioc/ORFik/man/ribosomeReleaseScore.html

Or something else ?

ADD COMMENTlink written 4 weeks ago by hauken_heyken40

Thanks! The ORFs are of bacteriophages. Could you please let me know among the links you sent which one would be suitable for bacteriophages? Thanks!

ADD REPLYlink written 4 weeks ago by DanielC90
1
gravatar for hauken_heyken
10 days ago by
hauken_heyken40 wrote:

If I understand then, you want to "Predict a mRNA's Translation Initiation Rate in Bacteria"

Go here and see if this is what you want ? https://salislab.net/software/predict_rbs_calculator

It would per gene, predict a RBS score (the translation initation rate)

Let me know if this is not what you want.

ADD COMMENTlink written 10 days ago by hauken_heyken40

Thanks! I need to do this for 200 ORFs that I predicted, can you please let me know how to use this calculator standalone?

ADD REPLYlink modified 10 days ago • written 10 days ago by DanielC90

Dear DanielC, your answers in this thread convey the impression of a bare minimum effort from your side.

ADD REPLYlink written 10 days ago by Carambakaracho1.6k

I dont understand what you mean, I just meant that it is a website to get the predictions, and I would like to know from where I can get this tool to download and use standalone. Can you let me know from where to download this tool for standalone use? Thanks for your reply!

ADD REPLYlink written 10 days ago by DanielC90
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