tRNALab

 

Installation files of tRNALab will be added to this website later.

 

There are two demos provided:

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Demo 1: Unzip inputs as a subdirectory of the directory where you have saved the executable of tRNALab. These inputs comprise input databases and settings, where #class = 4, FIRST_AA_IS_TESTED = 0, numOfTrimmedClassifications = 2, and NumOfMatingsAndMutations = 0 in order the computation gets very fast. Launch the simulation in a way that depend on your operating system:

 

Linux or macOS: In a terminal, change your directory to the place where you have saved the executable of tRNALab. Write: mpiexec -n 2 ./tRNALab

Windows: In Command Prompt or Developer Command Prompt for VS 2022, change your directory to the place where you have saved the executable of tRNALab. Write: mpiexec -n 2 tRNALab.exe

Visual Studio: Let a full path to the directory where you have saved the project of tRNALab be C:\path\tRNALab. Then source files are placed in C:\path\tRNALab\tRNALab and inputs.txt for a serial launch is loaded from C:\path\tRNALab\tRNALab\inputs, while the executable for a parallel launch is placed in C:\path\tRNALab\x64\Debug and so inputs.txt for a parallel launch is loaded from C:\path\tRNALab\x64\Debug\inputs. Launch Visual Studio and open tRNALab.sln. In Solution Explorer, unfold Source Files and double click on files within it. Then unfold Header Files and double click on files within it. Press F7 to compile the project. Then press one of the green arrows to launch tRNALab serially. Alternatively, you can launch the project in parallel from C:\path\tRNALab\x64\Debug according to the previous instructions.

 

In all cases described above, you will obtain demo1_job.out on a display and abe_L_classifications.txt in a directory outputs. If you did not obtain a resulting classification with ch_aaR_sim = 42.0872, try running tRNALab once again or perhaps even increase numOfTrimmedClassifications in settings.txt in a directory inputs. The full results of this demo with unconstrained input parameters is (1) on the website results.html.

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Demo 2:Unzip inputs as a subdirectory of the directory where you have saved the executable of tRNALab. These inputs comprise some input databases that were not in demo 1. a_tL_tDNA.txt consists of the average genes calculated from all Leipzig's archaeal tRNA genes using settings, b_tL_tDNA.txt are such test genes averaged from bacterial tRNA genes using settings, e_tC_tDNA.txt are calculated from the UCSC database of eukaryotic tRNA genes using settings, etc. You can even compute your own test databases using other settings. Because these test databases are small, you can make changes in them and then look how these changes affected simulation results.

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