Calculate Ribosome Binding Score for ORFs?

Question

[DanielC]

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.

Answer 1

[hauken_heyken]

Here: Python standalone implementation of RBS calculator.

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

[DanielC]

Thank you for this Hauken!

[DanielC]

Thanks! I ran this but, gave this error:

 python ../RBS_Calculator.py contig.fasta
Cutoff =  10
Traceback (most recent call last):
  File "../RBS_Calculator.py", line 1085, in <module>
    handle = open(filename,"rU")
IOError: [Errno 2] No such file or directory: '/common/RBS_Calculator/DataSets/All_Tested_RBSs.txt'

I see that there is no "common" directory in the git package? Could you please let me know where to get it or how to solve this issue? Thanks

Answer 2

[hauken_heyken]

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 ?

[DanielC]

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!

Answer 3

[hauken_heyken]

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.

[DanielC]

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

[Carambakaracho]

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

[DanielC]

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!