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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| TI2BioP_v2.0.rar | 2012-07-12 | 2.6 MB | |
| README.txt | 2012-07-11 | 2.2 kB | |
| Totals: 2 Items | 2.6 MB | 0 | |
The program version 2.0 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 I. 2D Nandy Graphs II. Linear representation (primary structure) III. Secondary structure inferred by the Mfold software * 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. * For the calculation of TIs from inferred secondary stuctures you must import CT files generated by the RNA STRUCTURE software * You can retrive the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs. 2. Click on the Aminoacids (AAs) button and you can select two types of protein representations for TIs calculation - 2D Nandy Graphs - Linear representation (primary structure) * Sequences can be uploaded to the program either one by one or you can import a FASTA file using the same format described above. Protein sequences can be represented with amino acids in one or three letter code. * Also you can choose the amino acid ponderations to be considered during TIs calculation * You can retrieve the results in an output file (txt) that can be easily uploaded into the excel or into other statistical programs 3. Click on the four-color map button and you can select the type of biopolymer (DNA, protein) for the TIs calculation * DNA and protein sequences can be uploaded and FASTA files imported in the same way described for the before modules * A drawing box is included to the user can see how four-color maps for DNA and proteins are built step by step. You may type the DNA or protein name and paste its sequence below and click add * Click One step button to see the first step in the four-color map construction for the selected sequence. Draw button shows the final four-color map. 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.