TI2BioP Files

TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS. The graphical interface starts by executing the "TI2BioP.pyw" file in the command line console

1. Decompress the .zip file
2. CD to the TI2BioP folder and: 
- Run "python3 setdata_AA.py" and "python3 setdata_NC.py" to create amino acid and nucleotide database
- Load the graphical interface (TI2BioP.pyw) by calling the interpreter (~python3 TI2BioP.pyw)
 

Python libraries/dependencies required

- Matplotlib
- numpy
- PyQT5
- Propy https://pypi.org/project/propy/


This version has been developed for speeding up the calculation of the Topological Indices (TIs) from a large amount of DNA/RNA and protein sequences, and for improving graph's visualization by using PyQt5 packages. 

1. Fasta files can be imported without any format restriction for the calculation of TIs from: 

I.  1D-DNA/RNA representations (primary structure) (click "Import DNA Seq" and select Process as: DNA/RNA and Apply "lineal"). Then click "TIs Calculation" button

II. 2D-DNA/RNA artificial or pseudo-folding structures: Nandy Graphs and Four-color maps (click "Import DNA Seq" and select Process as: DNA/RNA and Apply "Nandy Graph or Four-color map". Then click "TIs Calculation" button 

2. XFasta and CT files encoding 2D RNA structures can be imported for TIs calculation (click "Import RNA fasta" or "Import CT" buttons and select CT secondary structure). Then click "TIs Calculation" button

* You can select the nucleotide ponderations to be considered during TIs calculation. When you click "Ponderations", NEW nucleotide weights are listed.

You can retrieve the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs. Please introduce the directory and name at "Output filename"

3. For the calculation of protein TIs. Please click on the "Import AA seq" button, Process as "Amino acids" and then you can select two types of protein three types of protein representations
- Linear representation (primary structure)

- 2D Artificial representations: (i) 2D Nandy Graphs and (ii) Protein four-color maps

* Protein Sequences can be uploaded to the program as a FASTA file using "Import AA seq" button 
* Also you can choose the amino acid ponderations to be considered during TIs calculation. When you click "Ponderations", a list of referenced physico-chemical properties for the 20 natural aminoacid plus some non-frequent aas is provided. You can select any of them or all at the same time.
* You can retrieve the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs

4. A drawing box is included to display Nandy«s representation and four-color maps for DNA and proteins sequences.
- Protein Nandy's representation can be performed for several sequences at once while the four-color maps will be just draw for a single sequence. 

Otherwise, you may type the DNA or protein name and paste the sequences next to the "Add" button. Then apply "Nandy or Four-color maps" and click "Show" button

- The 2D artificial representation will pop up in a separated window.