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Subject name: Introduction To Bioinformatics |
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Author : Topic content : |
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Information revolution in Biology. Interrelationship of Bioinformatics and the other scientific disciplines. Physico-chemical properties of nucleic acids and amino acids. Application of Principal Component Analysis in the clustering of amino acids properties. Molecular evolution, population genetics and Bioinformatics. Genealogical trees and coalescence. Models of molecular evolution. Jukes-Cantor model for nucleic acids evolution. PAM model of protein evolution. Substitution and Scoring matrices: PAM, BLOSUM and log-odd matrices, and alignment score. Databases of genes and proteins, and their applications. Database of 3D structures of proteins: PDB. Protein family databases: CATH and SCOP Sequence alignment algorithms, alignment of pair and multiple sequences, local and global alignment. Database search. Phylogenetic methods. Distance matrices and clustering methods RNA database and Secondary structures of RNA • Consider the rapid expansion in the amount of biological sequence data available and compare this to the exponential growth in computer speed and memory size that has occurred; recognize why bioinformatics is now essential for understanding the information contained in the sequences and for efficient storage and retrieval of the information; • Explain some of the history of bioinformatics and demonstrate that many of its foundations are related to molecular evolution and population genetics; understand what is meant by the term “bioinformatics” and the role of bioinformatics in relation to other disciplines; • Describe the chemical and physical structure of nucleic acids and proteins; discuss the physico-chemical properties of the amino acids and their relevance in protein folding; • Use the amino acid property data as an example when introducing a statistical technique that are useful in bioinformatics: principal component analysis; • Explain some basic ideas in evolution and population genetics that provide a foundation for work in bioinformatics; discuss the role of mutation, natural selection, and random drift in molecular evolution; • Present the basics of the coalescence theory that describes the descent of individuals from common ancestors, and discuss the relevance of this theory to human evolution • Familiarize with the models of the evolution of nucleic acids and proteins; use these models in phylogenetic methods as the basis of defining evolutionary distances and calculating the likelihood of a set of sequences evolving on a phylogenetic tree; describe and interpret the details of these models; use the scoring systems in protein sequence alignment algorithms and also relate to evolutionary models; • Describe the derivation of PAM and BLOSUM substitution matrices in detail; break down the log-odd scoring matrices and the alignment score
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