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Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Introduction to Microbial Genomics.

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Presentation on theme: "Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Introduction to Microbial Genomics."— Presentation transcript:

1 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Introduction to Microbial Genomics An Introduction to Genomics Dave Ussery Biological Sequence Analysis DTU course # April, 2007

2 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

3 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Outline Introduction - where are we? Comparison of Genome Sizes The Human Genome Project A few words about speed of sequencing DNA repeats Brief intro. to genome atlases

4 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Where are we in the tree of life? Du står her

5 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU rRNA tree HUMANS rice (Oryza sativa ssp. japonica) 日欧先端科学セミナー ” 機能的ゲノム学 ” フォローアップワークショップ 2006年3月8日

6 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Algae Earth formed (~4.6 Bya) 4.5 Bya4.0 Bya3.5 Bya3.0 Bya2.5 Bya2.0 Bya1.5 Bya1.0 Bya0.5 Byatoday Oldest rocks Time (Billions of years ago, Bya) Oxygen levels rise Methanogenic Archaebacteria Sulfate reducing bacteria Single- celled eukarotes Edicaran fauna Cambrian Dinosaurs Oldest bacteria fossils Multi- cellular eukaryotes Bacterial ecosystems

7 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Earth formed (~4.6 Bya) 4.5 Bya4.0 Bya3.5 Bya3.0 Bya2.5 Bya2.0 Bya1.5 Bya1.0 Bya0.5 Byatoday Oldest rocks Time (Billions of years ago, Bya) Oxygen levels rise Bacteria Archaea 4.0 Bya Eukaryotic microbes ~2.0 Bya rice (Oryza sativa ssp. japonica) HUMANS

8 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU rRNA tree HUMANS rice (Oryza sativa ssp. japonica)

9 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

10 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

11 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU What is a genome?

12 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU  X174 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca

13 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Organism# bp#genes  -X Escherichia coli4,600, Saccharomyces cerevisiae13,000, Caenorhabditis elegans~100,000,000~14,000 Arabidopsis thaliana~120,000,000~10,000 Drosophila melanogastor~180,000,000~12,000 Homo sapiens~3,400,000,000~25,000

14 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

15 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU The Human Genome Project Started more than 20 years ago (~1985) The U.S. government agreed to invest $200,000,000 U.S. per year for 20 years. One base per second = 216 years! ~3,400,000,000 bp per haploid genome ~6,800,000,000 bp per diploid genome

16 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU year # human genes mapped #years to sequence human genome 1970nonenot possible 19803~4,000,000 years ~1000 years 2000~25,000draft 2005~30,000 new draft ,784 [Craig] 30,384 $1000 human genome + chimp, chicken, dog, mouse, pig, rat...

17 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Why is the human genome so large? One base per second = 216 years! ~3,400,000 bp per haploid genome ~6,800,000 bp per haploid genome Discussion questions: ~2% or less codes for proteins. Why is the human genome not finished yet?

18 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU fish insects higher plants jelly fish mammals birds Aristotle’s ladder of complexity minerals lower plants reptiles HUMANS

19 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

20 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU fruit- flies ferns humans minerals Database of Genome Sizes (DOGS) ladder of complexity lungfish cock - roaches

21 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU The “C-value paradox” The genome size of an organism is defined as the amount of haploid DNA in a genomic set (e.g., an egg or sperm nucleus). This is also referred to as the "C-value"; the "C" means "constant" or "characteristic", since the size of a genome is usually constant for a given species. The large difference in genome sizes without any seeming relation to an organism’s complexity, is called the C-value paradox.

22 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU What does all this DNA do? 90% 50% 2% <1%

23 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU The approximate size and characteristics of genomes was characterised in the 1960s, in a classic study of the kinetics of DNA reassociation by Britten and Kohne (1968). 1. foldback DNA 2. highly repetitive DNA 3. middle-repetitive DNA 4. single-copy DNA The repetitive DNA can either be localised to discrete regions, or dispersed. They found that the DNA could be divided into four fractions: Britten,R.J., Kohne,D.E., "Repeated sequences in DNA", Science, 161: , (1968). DNA repeats

24 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Highly repetitive DNA Dispersed - e.g., Alu family about 300 bp long 500,000 copies in humans (about 5% of the human genome) dispersed throughout the chromosomes Localised highly repetitive sequences about 2-10 bp long present in millions of copies, often in large blocks (about 6% of the human genome) associated with heterochromatin usually very high A+T content

25 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Often, satellite DNA consists of long tandem arrays of repeated sequences, all localised to one or a few discrete regions in the chromosomes. For example, in the kangaroo rat (Dipodomys ordii), more than 50% of the genome consists of three families of repeated sequences: Localised repetitive DNA (AAG) n, where n = ~2.24 x 10 9 (TTAGGG) n, where n = ~2.2 x 10 9 (ACACAGCGGG) n, where n = ~1.2 x 10 9

26 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Middle repetitive DNA makes up more than 40% of the human genome position varies due to transposable elements Includes the following types of sequences: - Dinucleotide repeats - microsatellite DNA - TRInucleotide repeats - associated with many diseases - ( e.g., Fragile X, muscular distrophy)

27 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU What about bacteria?

28 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

29 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

30 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU A decade of sequencing prokaryotic genomes. Number Genomes Published Year

31 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Kronborg Castle

32 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

33 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

34 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

35 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU What is Bioinformatics? Bioinformatics is the application of machine learning processes to biological information.

36 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU The science of information and information flow in biological systems, esp. the use of computational methods in genetics and genomics. bioinformatics, n.

37 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

38 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU What is Biological Information? Genome -> Transcriptome ->Proteome

39 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

40 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

41 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?

42 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU  X174 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca

43 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

44 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU

45 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU Summary 1. A “genome” is sum of all the DNA sequences (chromosomes) in an organism. 2. The sizes of genomes range about 100,000,000 fold - from small viruses to very large amoebas. 3. Many eukaryotic genomes contain large fractions of repeated DNA sequences, and there is no apparent correlation between the size of an organism and its biological complexity (”C-value Paradox”) 4. Sequence databases are growing faster than computational power!

46 Comparative Microbial Genomics group Center for Biological Sequence Analysis The Technical University of Denmark DTU


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