Algorithms for Molecular Biology (MATE8990)

Latest Course Syllabus-ABET Style () (PDF)

Credits: 3
Students should take this course at: 1st Year - 2nd Semester


Topics covered will include biological sequences, assembly, sequence alignments, sequence phylogeny, sequence database searches, gene prediction, and whole genome analysis, including transcriptome and microarray analysis, gene clustering and application of statistics to gene profiling data. We will emphasize the fundamental theory behind the analysis, and also present practical problems and their solutions. The course will use open–source bioinformatics tools, and show how to construct such tools using biopython, a set of libraries for bioinformatics in the python programming language. The course is designed for graduate and advanced undergraduate students in computer science. A basic knowlege of biology is assumed. Students from other disciplines are invited to participate, but will have to make up the background.


  • Introduction: History of Bioinformatics

  • Ethical Issues in Bioinformatics

  • Sequences: Nucleic Acids and Proteins

  • Collecting and Storing Sequences

  • Computer platforms used in sequence analysis

  • Sequence features, Promoters, etc.

  • Gene order

  • Pairwise and Multiple Sequence Analysis

  • Database Searching for Similar Sequences

  • Phylogeny

  • Functional Genomics: Microarrays

  • Statistical Methods for Analysis of Microarray Data

  • Gene Clustering Analysis

  • Defining Gene Regulatory Networks: Reverse Engineering


  • Introduce students to fundamental concepts in bioinformatics, programming, algorithm design and analysis.

  • Be able to select tools and programs to solve bioinformatic problems and participate in their development.