michael schroeder biotechnological center tu dresden biotec discrete algorithms for computational...
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Michael Schroeder BioTechnological CenterTU Dresden Biotec
Discrete Algorithms for Computational Biology
Gene Myers, MPI-CBGMichael Schroeder, Biotec, TUD Dresden
Michael Hiller, MPI-CBG
By Michael Schroeder, Biotec 2
Bioinformatics
BIOlogy
matheMATICS
INFORmatics
By Michael Schroeder, Biotec 3
Bioinformatics
Bioinformatics = Biological + Informatics
By Michael Schroeder, Biotec 4
Bioinformatics
Bioinformatics = Biological + Informatics - Logical
Synopsis
Computational problems and algorithmic solutions for genomic data Pre-requesite: Data structure and basic algorithms
Goal: (a) able to design a dynamic programming (b) understand sequence comparison and Hidden
Markov Model methods (c) understand, use, and programme sequence-based
bioinformatics
By Michael Schroeder, Biotec 5
Part 1: Sequence comparison
Week 1: Primer on Molecular Biology Week 2-5: Sequence Comparison, theory and
practice The basic dynamic programming algorithm, gap cost
variations, extension to patterns. Acceleration: indexing, filtration methods, FASTA and
BLAST as examples. Multi-sequence alignment: scoring schemes,
greedy/DCA/MSA/round-robin heuristics.
By Michael Schroeder, Biotec 6
Part 2: Gene Finding
Week 6-9: Gene Finding Approaches: statistical, homology-based, Bayesian via
Hidden Markov Models. Hidden Markov Models (HMMs): Viterbi and
forward/backward algorithms
By Michael Schroeder, Biotec 7
Part 3: Phylogeny
Week 10-13: Phylogeny Jukes-Cantor model, maximum-likelihood method,
distance-based methods, neighbor-joining, HMMs. Genome rearrangements
By Michael Schroeder, Biotec 8
Part 4: Optional topics
Week 14: Optional Topics (per instructor and time permitting) RNA Secondary Structure: Definitions, Scoring
schemes, dynamic programming approaches. Motif Finding: Repeat finding. Promoter and enhancer
recognition. Signal peptide recognition. Genotyping: Basic genetics, haplotype determination,
haplotype blocks, forensic identification. Genome Sequence Assembly: Technology overview.
Overlap-layout-consensus paradigm. Approaches.
By Michael Schroeder, Biotec 9
By Michael Schroeder, Biotec 10
Getting in touch
Email: [email protected]
Web site: http://www.biotec.tu-dresden.de/schroeder
By Michael Schroeder, Biotec 11
Useful books