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| CS 57900 - Bioinformatics Algorithms |
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Credit Hours: 3.00. Review of Genomes, DNA, RNA, proteins, proteomes. Biological Sequences: dynamic programming; pairwise global, local, and semi-global alignments of genes and proteins; constant, affine, and general gap penalties; RNA alignments; BLOSUM and PAM scoring matrices. Multiple alignment of proteins: approximation algorithms; iterative and progressive alignment methods. Database search for sequences: BLAST and variants. Phylogentic Trees: distance-based methods, ultrametric and additive distance functions; parsimony, and maximum likelihood methods. Whole Genome Alignment: suffix trees and suffix arrays. Systems Biology: Module discovery in biological networks, spectral algorithms for graph clustering. Network alignment: quadratic programming formulations and graph matching. Genetic Variation: haplotype inference, the perfect phylogeny problem and chordal graphs. Additional topics such as next-generation sequencing, analysis of multidimensional data from flow cytometry, and gene expression data, if time permits. Typically offered Fall.
3.000 Credit hours Syllabus Available Levels: Undergraduate, Graduate, Professional Schedule Types: Lecture Offered By: College of Science Department: Computer Science Course Attributes: Upper Division May be offered at any of the following campuses: West Lafayette Learning Outcomes: 1. Students will learn how to design algorithms. 2. Students will learn how to solve computational problems from the new biology, the data-rich field that biological sciences is becoming. |
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