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Oct 17, 2026
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2026-2027 University Catalog
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CS 57900 - Bioinformatics Algorithms
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. Phylogenetic 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.
Learning Outcomes
1. Learn how to design algorithms. 2. Learn how to solve computational problems from the new biology, the data-rich field that biological sciences is becoming.
Credit Hours: 3.00
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