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Algorithms for Biosequence Comparison

Biology And Biomedical Sciences 5504 - Spring 2020

This course surveys algorithms for comparing and organizing discrete sequential data, especially nucleic acid and protein sequences. Emphasis is on tools to support search in massive biosequence databases and to perform fundamental comparison tasks such as DNA short-read alignment. These techniques are also of interest for more general string processing and for building and mining textual databases. Algorithms are presented rigorously, including proofs of correctness and running time where feasible. Topics include classical string matching, suffix array string indices, space-efficient string indices, rapid inexact matching by filtering (including BLAST and related tools), and alignment-free algorithms. Students complete written assignments and implement advanced comparison algorithms to address problems in bioinformatics. This course does not require a biology background. Prerequisites: CSE 347 or instructor permission Revised: 2019-02-21
Course Attributes: EN TUEN BME T2

Section 01

Algorithms for Biosequence Comparison
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