| Biography | |
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 Prof. Ali Iranmanesh Tarbiat Modares University, Iran |
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| Title: Applications of Graph Data Structures in Comparative Genomics | |
| Abstract: Comparative genomics is a field of biology where the genome of different species are compared to each other to understand evolutionary and molecular differences between species. Multiple genome alignment is an indispensable tool for comparing genomes and finding their shared histories. This talk presents an overview on the different approaches for multiple genome alignment methods with focusing on application of graph data structures. In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA or protein to identify regions of similarity that may be a consequence of functional, structural or evolutionary relationships between the sequences. Genome sequence alignment problem try to uncover homologies by assigning sequence positions. As an effective modeling, analysis and computational tool, graphs are widely used in bioinformatics to deal with various biological problems. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments and also provide an intuitive representation of similarities and changes between genomes. In addition by having a graph data structure for a multiple genome alignment, it is possible to model colinear and non-colinear changes without the need of choosing a reference genome. Each multiple alignment can be represented as an alignment graph of sequence segments. Let G = (V,E) be an alignment graph data structure, for a set S = {S_1,S_2,…,S_n} of n sequences, G = (V,E) is an n-partite graph for n sequences where the vertices represent non overlapping sequence segments, then V = V_1∪ V_2 ∪… ∪ V_n and each vertex v_ij ∈ V_i represents a sequence segment in S_i of arbitrary length which covers all positions of the segment. Every position in S_i = S_(i_1 ) S_(i_2 ) … S_(i_(|Si| ) )is covered by one and only one vertex vij ∈ V_i , where 1<i<n ,1<j<|S_i |. An edge e = (v_ip ,v_jq)∈ E with i ≠ j indicates that vertex vip can be aligned with vertex v_jq . In other words, the sequence substring in S_i covered by v_ip can be aligned without gaps to the substring in S_j covered by v_jq. This graph structure can be a weighted graph by edge weights that capture some kind of quantitative measure of alignment quality. The score of aligning v_ip with v_jq is given by edge weight of e.This talk describes most commonly used graph data structures in terms of their abilities to represent alignment information. | |
| Biography: Ali Iranmanesh received his Ph.D. degree from the University of Tarbiat Modares, Tehran, Iran, in 1995. Since 1995 he has been employed in the same university and from 2005, he is a full professor of mathematics. His research interests are Character theory of finite groups, application of group theory in Chemistry, Mathematical Chemistry, BioMathematics, nano computation, hyperstructures and applications, history of Mathematics and education of Mathematics. At present, he is Editor in chief of the Iranian Journal of Mathematical Sciences and Informatics and also he is a member of Academy of Mathematical Chemistry. Recently, he is elected as a Distinguished Professor of Iranian Universities by Ministry of Science, Research and Technology. | |
