Title Center for Biological Sequence Analysis The Technical University of Denmark DTU Part 3: DNA Repeats In Bacterial Genomes Comparative Microbial Genomics.

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Presentation transcript:

title Center for Biological Sequence Analysis The Technical University of Denmark DTU Part 3: DNA Repeats In Bacterial Genomes Comparative Microbial Genomics Group Dave Ussery Advanced Bioinformatics course lecture 14 November, 2003

Outline Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU Outline DNA Repeats in Bacterial Genomes Introduction Global Repeats Local Repeats Cruciforms

DNA info? Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU The DNA sequence contains information. But what kind of information?

Alternative structures Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Repeats defined Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU CHRO2003 DNA Symmetry Elements Defined What are symmetry elements? REPEATS in DNA Sequences Direct repeats 5’ GGGAATNNGGGAAT 3’ 3’ CCCTTANNCCCTTA 5’ Inverted repeats 5’ GGGAATNNATTCCC 3’ 3’ CCCTTANNTAAGGG 5’

Ecoli Genome Atlas Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Ecoli repeats atlas Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Ecoli pO157 Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

pX01 cruci - cover Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

pVir genome Atlas Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU CHRO2003

pWR501 Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

pCP301 Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Repeats table Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Direct Repeats Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Inverted Repeats Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Mirror Repeats Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Everted Repeats Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

4 Summary Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU

Summary 1. DNA sequence  DNA structure  Function summary Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU 2. Where you are in the chromosome is important!