A Computational Method to select Optimal Nucleotide Position for Site-specific Mutagenesis to downregulate overexpression in Myc gene
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A ppt version of the transparencies I used as the final presentation for a project under Prof. S. K. Ray. The project was on "A Computational Method to select Optimal Nucleotide Position for Site-specific Mutagenesis to downregulate overexpression in Myc gene"
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QSAR STUDY ON READY BIODEGRADABILITY OF CHEMICALS. Presented at the 3rd Chemo...
A Computational Method to select Optimal Nucleotide Position for Site-specific Mutagenesis to downregulate overexpression in Myc gene
- 1. A Report on A Computational Method to select Optimal Nucleotide Position for Site-specific Mutagenesis to downregulate overexpression in Myc gene Submitted by Mustafa Safdari 2005P7PS015 For Partial Fulfillment of BITS GC 331: Computer Project Under the guidance and supervision of Prof. S. K. Ray Biological Sciences Department BITS, Pilani – Goa Campus 1st Semester 2008 – 2009
- 3. Study of cancer causing effects in genes
- 4. Physicochemical properties of genes
- 5. Characterization of genes based on these properties
- 6. Use of this Characterization
- 8. Drawbacks with current state-of-the-art
- 9. Project Aim
- 12. Simulation and analysis of results
- 14. Cross Product: considering each nucleotide triplet as a codon vector, find out the codon vectors of both the sequences with their centroids as their reference origin. Convert each of these vectors into unit vectors. Perform cross product of all these vectors, taking unit vector at each stage. Calculate the distance between the two resultants, naming it DISTANCE1 Consider each codon in the mutated sequence one at a time, from the beginning to the end. Create a newly modified sequence, which is a copy of the mutated sequence, except for the difference of this one codon where we substitute it with one of its degenerate codon. Perform the same steps 1 through 4 with the 2 sequences as the original normal and the newly modified sequence. Calculate the distance between the original normal sequence and this newly modified sequence naming it DISTANCEkj. From the list of all the DISTANCEkj obtained, select the option with the least DISTANCEkj. This is the solution to the problem which brings the newly modified gene closest to the original normal gene in terms of functionality.
- 15. The codons in the sequence are represented as points are distributed in the 3-D space. This is the centroid of this mutated gene sequence of codons
- 16. This is the centroid or the point depicting the characteristic value of the mutated sequence. This is the centroid or the point depicting the characteristic value of the original normal sequence. This region of green dots represents possible feasible solutions with characteristic points nearer to the original normal centroid than the mutated one. This region of black dots represents possible feasible solutions with characteristic points farther to the original normal centroid than the mutated one.