TI2BioP Files

The program consists in three modules for the calculation of the Topological Indices (TIs)for DNA/RNA sequences
1. Click on the DNA_RNA button and you may select three different representations for DNA/RNA sequences
- 2D Nandy Graphs
- Linear representation (primary structure)
- Secondary structure inferred by the Mfold software
2. Sequences can be inputed to the program either one by one or you can import a FASTA file containing sequences IDs followed by additional information (source and gene name) between square brakets or parentheses.
3. For the calculation of TIs from inferred secondary stuctures you must import CT files generated by the RNA STRUCTURE software 
4. You can retrive the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs.

So far, two modules for the calculation of the TIs to protein sequences have been implemented
1. Click on the Aminoacids (AAs) button and you can select two types of representations for proteins
- 2D Nandy Graphs
- Linear representation (primary structure)
- Four color maps are under development
2. Sequences can be inputed to the program either one by one or you can import a FASTA file using the same format described above. Protein sequences can be repesented with aminoacids in one or three letter code.
3. Also you can choose the aminoacid ponderations to be considered during TIs calculation 
4. You can retrive the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs.

In the code button you can find the 20 natural aminoacid plus some non-frequent aas in one and three letter code.
A list of referenced physico-chemical properties for the aas is provided as well.