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Computational Biology
Nives Skunca
Slides prepared by Dr. Christophe Dessimoz
Q
Introduction, Basic Biology
19/21 Septemb...
This week
Course introduction
Basic Biology
Reality
Nature
observation
observation
observation
perturbation
take it apart
“in vitro”
recreate life
“synthetic biology”...
Learning Outcomes
• Understand basic concepts of molecular
biology
• Understand and apply fundamental
models, algorithms, ...
Topics
Molecular Genetics
Gene Evolution
Genome Evolution
Mass Spectrometry
Codon Bias
Modeling
Dynamic programming
Markov...
Organization
• Lecture
• Wed 13-14 (CAB G52), Fri 13-15 (ML F34)
• Prof. Gonnet will hold the lectures
• Exercises:
• Thu ...
Teaching Assistants
• Stefan Zoller
• Nives Skunca
Date Topic Lecturer
Sept. 19/21 Course Introduction; Basic Molecular
Biology
NS
Sept. 26/28 Markov models/String Alignment...
Course Grade & Credits
• Participation in the exercises is strongly
encouraged, but not mandatory
• Written Exam
• During ...
Course Homepage
• Course details
• Schedule
• Slides
• Exercises
http://www.cbrg.ethz.ch/education/CompBiol
Darwin
• Interpreted language based on Maple
• Environment for bioinformatics, can do
sequence management, mathematics,
al...
Biorecipes
• A collection of real
problems with coded
solutions in the
Darwin language
• Darwin input in green
• Darwin ou...
Other materials
• Slides can be downloaded from the
course homepage.
• Additional notes and references will be
made availa...
Basic Biology
Slides of this part are largely
based on material from
Dr. Gina Cannarozzi
Basic Principles
• Universality of life on earth: water,
carbon-based biochemistry; genetic
material; genetic code (largel...
So what is life?
• What about endospores? viruses? mules? priests?
prions? computer viruses?
• In biology, there are excep...
Inside a Cell
http://www.osovo.com/diagram/prokaryoticcelldiagram.htm http://www.biologycorner.com/resources/cell.gif
Euka...
Relevant components
• Ribosomes translate mRNA into proteins.
• Mitochondria (eukaryotes) have their own
DNA and are a res...
• Genome: all the genetic
material of an organism.
• The genome consists of
genes and non-coding
regions.
• Genes consist ...
Escherichia coli Homo sapiens
1 circular chromosome
1 plasmid (multiple copies)
~4.6 million base pairs
~3.9 million
codin...
DNA
Deoxyribonucleic acid
• Double helix
• Backbones: phosphate and
deoxyribose , directed
(5’ → 3’), antiparallel
• Conne...
DNA Bases
Wikipedia
PuRines
PYrimidines
C ···· G: 3 H-bonds
A ···· T: 2H-bonds
Hydrogen Bond
• X-H ···· Y where X,Y is
an electronegative
atom (typically N,O,F)
• Responsible for high
boiling point of ...
“Central dogma of
molecular biology”
Wikipedia
DNA Replication
Wikipedia
Polymerase can only add bases from 5’→3’
(DNA is read 3’ → 5’)
Movie time!
Replication visualized:
http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/
End of day 1
RNA
• Single stranded (can form structure)
• Uracil instead of Thymine
• mRNA: messenger RNA, for translation
• rRNA: subu...
Transcription
• Transcription factors bind to promoter sites at
the 5’ regulatory region.
• RNA polymerase, binds to the c...
Roger Kornberg
Nobel Prize Chemistry 2006
The chain shown in grey is RNA polymerase,
with the portion that clamps on the D...
Post-transcriptional
modifications (Eukaryotes)
• 5’ Cap
• Poly-A tail
• Splicing (removal of introns)
Research questions:...
Alternative Splicing
• Humans: >50% of genes have splice variants.
• Dscam gene in D. melanogaster: 95 alternative
exons c...
Translation
Wikimedia
Commons
The Genetic Code
Proteins
• Participate in most (all?) cellular processes
• Made of 20 amino-acids (+ occasionally a
cofactor, such as meta...
Functions of Proteins
Albertsetal.,“Essentialcellbiology:anintroductiontothe
molecularbiologyofthecell”,Garland1996
...
Amino
Acids
Wikimedia
Commons
• Only sidechains
differ (red)
• Sidechains have
diverse chemical
properties
(charge, size, ...
Peptide Bond
G. Cannarozzi
Proteins
have a 3D
structure
Wikimedia Commons
Biological sequences
How are they identified?
Where are they stored?
Next Generation Sequencing
e
MDISTLTASEEIE
MEIDAEEIEIMAT
IDLAEDLISLFM
DDMFSSIDLESI
NFEIFNSSDIDSI
NIDLESIEEIEIMF
EEIEIMATIFNSS
DIDIMMDIMMD
SINFEIFNSSD...
Growth of sequence databases
0
0.5
1.0
1.5
2.0
2000 2002 2004 2006 2008 2010 2012
Year
Numberofsequencesx10^7
Protein Data...
Getting Sequences
Ensembl
...
e.g. GenBank File
e.g. GenBank
File
e.g. GenBank File
Evolution
Darwinian Evolution
• Start from an initial population
• Repeat:
• reproduce and “mutate” randomly
• natural selection: fi...
Not only the “good”
characters survive
• Genetic drift (random sampling)
• Population bottleneck
• Founder effect
• Geneti...
Species Evolution
• Speciation: the
evolutionary process by
which new species arise
• Can occur from
geographic isolation ...
Krzywinski et al. Circos: an information aesthetic for comparative genomics. Genome Research (2009) vol. 19 (9) pp. 1639-4...
Example: recombination
among E. coli strains
Mau et al. Genome Biology 2006 7:R44
Whole genome duplications
Gene Evolution
Kunkel, 2004,The Journal of Biological Chemistry
Point mutations
Point mutations
Purines
Pyrimidines
Insertion/deletion
Lateral Gene
Transfer
Wikipedia
http://www.scq.ubc.ca/attack-of-the-superbugs-antibiotic-resistance/
Recombination
Gene Evolution
• Mutation (base substitution)
• Insertion/Deletion
• Transposition (horizontal transfer)
• Recombination
•...
Evolutionary Distances
• Time since divergence
• Number of common traits.
• Edit distance (minimum # of elementary
operati...
Markovian Evolution
Markov Model: every site evolves independently,
probability of mutation only depends on present
state ...
http://gi.cebitec.uni-bielefeld.de/people/boecker/bilder/tree_of_life_new.gif
Augustin Augier,
Arbre Botanique
(1801)
Lamarck, Philosophie Zoologique , 1809
Darwin, Notebook B, 1837
Edward Hitchcock, Elementary Geology, 1840
Haeckel,The Evolution of Man, 1879
rRNA was used by Woese (1987) to group early life forms into
three kingdoms
THEMA
CENSY
METKAMETJAMETMP
METTHMETS3
METST
ARCFU METHJ
METMJ
METLZ
UNCMA
METAC
METMAMETBF
METBU
METTP
HALWD
NATPDHALMAHA...
KLULA
YEAST
CANGA
PICST
DEBHA
CANAL
LODEL
SCHPO
CRYNE
USTMA
APIME
DROME
DROPS
ANOGA
AEDAE
CHICK
ORNAN
LOXAF
ECHTE
DASNO
MY...
L1 intro biology-pdf
L1 intro biology-pdf
L1 intro biology-pdf
L1 intro biology-pdf
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L1 intro biology-pdf

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L1 intro biology-pdf

  1. 1. Computational Biology Nives Skunca Slides prepared by Dr. Christophe Dessimoz Q Introduction, Basic Biology 19/21 September 2012
  2. 2. This week Course introduction Basic Biology
  3. 3. Reality Nature observation observation observation perturbation take it apart “in vitro” recreate life “synthetic biology” obs. obs. perturb. obs. obs. perturb. Catalogue Georg Dionysius Ehret's illustration of Linnaeus's sexual system of plant classification, 1736 Model f(x) formulate/select Validate by simulation Validate on real data prediction Estimate
  4. 4. Learning Outcomes • Understand basic concepts of molecular biology • Understand and apply fundamental models, algorithms, data structures, and computational techniques to answer biological questions • Wide range of topics, but special focus on biological sequences and their evolutionary context.
  5. 5. Topics Molecular Genetics Gene Evolution Genome Evolution Mass Spectrometry Codon Bias Modeling Dynamic programming Markov models Least squares Maximum Likelihood Optimization Heuristics Simulation x
  6. 6. Organization • Lecture • Wed 13-14 (CAB G52), Fri 13-15 (ML F34) • Prof. Gonnet will hold the lectures • Exercises: • Thu 14-16 (CAB H56), starting this week • If you do not have a nethz account, ask Stefan Zoller as soon as possible.
  7. 7. Teaching Assistants • Stefan Zoller • Nives Skunca
  8. 8. Date Topic Lecturer Sept. 19/21 Course Introduction; Basic Molecular Biology NS Sept. 26/28 Markov models/String Alignment I GHG Oct. 3/5 String Alignment II (indels, estimating distances) GHG Oct. 10/12 Substitution Matrices GHG Oct. 17/19 Approximate Alignment Methods; Statistics of Pairwise Alignments GHG Oct. 24/26 Phylogeny I GHG Oct.31/Nov.2 Phylogeny II GHG Nov. 7/9 Phylogeny III GHG Nov. 14/16 Multiple Sequence Alignments AS Nov. 21/23 Synthetic Evolution; Evaluation of Estimators DD/GHG Nov. 28/30 Current research; Mass profiling Guests/ GHG Dec. 5/7 Orthology/Lateral Gene Transfer NS Dec. 12/14 Codon bias SZ Dec. 19/21 Genome Rearrangements GHG
  9. 9. Course Grade & Credits • Participation in the exercises is strongly encouraged, but not mandatory • Written Exam • During winter session • 3 hours • Only support materials are 2 A4 pages (4 sides), personally handwritten.
  10. 10. Course Homepage • Course details • Schedule • Slides • Exercises http://www.cbrg.ethz.ch/education/CompBiol
  11. 11. Darwin • Interpreted language based on Maple • Environment for bioinformatics, can do sequence management, mathematics, alignments, trees, drawing, etc. • Available for download mac and linux (http://www.cbrg.ethz.ch/darwin)
  12. 12. Biorecipes • A collection of real problems with coded solutions in the Darwin language • Darwin input in green • Darwin output in red www.biorecipes.com
  13. 13. Other materials • Slides can be downloaded from the course homepage. • Additional notes and references will be made available as well.
  14. 14. Basic Biology Slides of this part are largely based on material from Dr. Gina Cannarozzi
  15. 15. Basic Principles • Universality of life on earth: water, carbon-based biochemistry; genetic material; genetic code (largely) universal. → common origin! • Life is compartmentalized: cells are fundamental units of structure, function, organization • Self-replicating • Capable of Darwinian evolution 10 µm Cryptomonadales Encyclopedia of Life (eol.org)
  16. 16. So what is life? • What about endospores? viruses? mules? priests? prions? computer viruses? • In biology, there are exceptions to almost every rule. “Living organisms undergo metabolism, maintain homeostasis, possess a capacity to grow, respond to stimuli, reproduce and, through natural selection, adapt to their environment in successive generations.”
  17. 17. Inside a Cell http://www.osovo.com/diagram/prokaryoticcelldiagram.htm http://www.biologycorner.com/resources/cell.gif EukaryoteProkaryote 10-30 µm~2 µm
  18. 18. Relevant components • Ribosomes translate mRNA into proteins. • Mitochondria (eukaryotes) have their own DNA and are a result of early inclusion of α- proteobacteria into a eukaryotic cell. • Chloroplasts (plants, protists) have their own DNA as a result of early inclusion of cyanobacteria into a eukaryotic cell. • Plasmids (bacteria) are short pieces of circular DNA in multiple copies; nonessential; get transferred between bacteria.
  19. 19. • Genome: all the genetic material of an organism. • The genome consists of genes and non-coding regions. • Genes consist of regulatory regions, intron, exons, untranslated regions http://www.scfbio-iitd.res.in/tutorial/geneorganization.html Genome chromosome chromatin histone
  20. 20. Escherichia coli Homo sapiens 1 circular chromosome 1 plasmid (multiple copies) ~4.6 million base pairs ~3.9 million coding bases (85%) 4132 protein-coding genes 172 RNA (tRNA, rRNA,etc) 578 pseudogenes 23 chromosome pairs ~3 billion base pairs ~50 million coding bases (1.5%) ~21,000 protein-coding genes ~294,000 exons ~60,000 different transcripts ~6,000 pseudogenes ~4,800 RNA genes ~2,900 RNA pseudogenes
  21. 21. DNA Deoxyribonucleic acid • Double helix • Backbones: phosphate and deoxyribose , directed (5’ → 3’), antiparallel • Connection: 4 bases Adenine, Thymine, Cytosine, Guanine. • A-T and C-G are paired by hydrogen bonds (relatively weak) Wikipedia 34 Å (3.4 nm) 3.3 Å (0.33 nm)
  22. 22. DNA Bases Wikipedia PuRines PYrimidines C ···· G: 3 H-bonds A ···· T: 2H-bonds
  23. 23. Hydrogen Bond • X-H ···· Y where X,Y is an electronegative atom (typically N,O,F) • Responsible for high boiling point of water (each H20 can have up to 4 H bonds)
  24. 24. “Central dogma of molecular biology” Wikipedia
  25. 25. DNA Replication Wikipedia Polymerase can only add bases from 5’→3’ (DNA is read 3’ → 5’)
  26. 26. Movie time! Replication visualized: http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/
  27. 27. End of day 1
  28. 28. RNA • Single stranded (can form structure) • Uracil instead of Thymine • mRNA: messenger RNA, for translation • rRNA: subunit of ribosome • tRNA: specific for one amino-acid, selectively bind to codon via ribosome. • microRNA: short nucleotides (~22 nts) which regulate gene function http://www.pdb.org/pdb/static.do? p=education_discussion/ molecule_of_the_month/pdb15_2.html
  29. 29. Transcription • Transcription factors bind to promoter sites at the 5’ regulatory region. • RNA polymerase, binds to the complex. • Working together, they open the DNA double helix. • Genes can be on either strand, but direction of growing mRNA sequence is always 5’ → 3’
  30. 30. Roger Kornberg Nobel Prize Chemistry 2006 The chain shown in grey is RNA polymerase, with the portion that clamps on the DNA shaded in yellow.The DNA helix being unwound and transcribed by RNA polymerase is shown in green and blue, and the growing RNA stand is shown in red. http://med.stanford.edu/featured_topics/nobel/kornberg/release.html
  31. 31. Post-transcriptional modifications (Eukaryotes) • 5’ Cap • Poly-A tail • Splicing (removal of introns) Research questions:Where are the introns? Where are the coding sequences? Where are the stop and start of transcription? Where are the binding sites for the transcription factors that control when transcription takes place?
  32. 32. Alternative Splicing • Humans: >50% of genes have splice variants. • Dscam gene in D. melanogaster: 95 alternative exons can express 38,016 different mRNAs through alternative splicing.
  33. 33. Translation Wikimedia Commons
  34. 34. The Genetic Code
  35. 35. Proteins • Participate in most (all?) cellular processes • Made of 20 amino-acids (+ occasionally a cofactor, such as metal ion, heme, ATP, etc.) • Encoded in DNA
  36. 36. Functions of Proteins Albertsetal.,“Essentialcellbiology:anintroductiontothe molecularbiologyofthecell”,Garland1996 ...
  37. 37. Amino Acids Wikimedia Commons • Only sidechains differ (red) • Sidechains have diverse chemical properties (charge, size, pH, hydrophobicity, ...)
  38. 38. Peptide Bond G. Cannarozzi
  39. 39. Proteins have a 3D structure Wikimedia Commons
  40. 40. Biological sequences How are they identified? Where are they stored?
  41. 41. Next Generation Sequencing
  42. 42. e MDISTLTASEEIE MEIDAEEIEIMAT IDLAEDLISLFM DDMFSSIDLESI NFEIFNSSDIDSI NIDLESIEEIEIMF EEIEIMATIFNSS DIDIMMDIMMD SINFEIFNSSDIDI MMDATIDLAED LISLFMDDMFSS IDLESINFEIFNSS Sequence Database ...AEDLISLFMDDM ... Protein Identified Unidentified protein extracted from gel Split into fragments of 5-10 amino acids Determine mass using MS (Mass Spectrometry) Determine amino acid sequence and compare with sequ- ence database Proteomics Jiang Long, Science Creative Quarterly Image Bank
  43. 43. Growth of sequence databases 0 0.5 1.0 1.5 2.0 2000 2002 2004 2006 2008 2010 2012 Year Numberofsequencesx10^7 Protein Data Bank UniProtKB/TrEmbl
  44. 44. Getting Sequences Ensembl ...
  45. 45. e.g. GenBank File
  46. 46. e.g. GenBank File
  47. 47. e.g. GenBank File
  48. 48. Evolution
  49. 49. Darwinian Evolution • Start from an initial population • Repeat: • reproduce and “mutate” randomly • natural selection: fittest individuals survive and have descendants → selects “good” mutations • sometimes: a “branching” occurs (e.g. speciation, duplication)
  50. 50. Not only the “good” characters survive • Genetic drift (random sampling) • Population bottleneck • Founder effect • Genetic hitchhiking (neutral or mildly deleterious alleles linked to positively selected gene)
  51. 51. Species Evolution • Speciation: the evolutionary process by which new species arise • Can occur from geographic isolation or barriers, new niche entered, animal husbandry Diane Dodd’s fruit fly experiment http://evolution.berkeley.edu/evolibrary/article/_0_0/evo_45
  52. 52. Krzywinski et al. Circos: an information aesthetic for comparative genomics. Genome Research (2009) vol. 19 (9) pp. 1639-45 Genome Rearrangements e.g. Human vs. Dog
  53. 53. Example: recombination among E. coli strains Mau et al. Genome Biology 2006 7:R44
  54. 54. Whole genome duplications
  55. 55. Gene Evolution
  56. 56. Kunkel, 2004,The Journal of Biological Chemistry Point mutations
  57. 57. Point mutations Purines Pyrimidines
  58. 58. Insertion/deletion
  59. 59. Lateral Gene Transfer Wikipedia
  60. 60. http://www.scq.ubc.ca/attack-of-the-superbugs-antibiotic-resistance/
  61. 61. Recombination
  62. 62. Gene Evolution • Mutation (base substitution) • Insertion/Deletion • Transposition (horizontal transfer) • Recombination • Gene loss or gene duplication • Splicing pattern mutations
  63. 63. Evolutionary Distances • Time since divergence • Number of common traits. • Edit distance (minimum # of elementary operations to transform one object into the other) • ... • Desirable properties • distance estimable without knowing history • metric properties (e.g. triangle inequality) How can we quantify the amount of evolution between two subjects?
  64. 64. Markovian Evolution Markov Model: every site evolves independently, probability of mutation only depends on present state (no memory), probabilities of mutation are expressed by transition matrix. A C G T A 0.900 0.033 0.033 0.033 C 0.033 0.900 0.033 0.033 G 0.033 0.033 0.900 0.033 T 0.033 0.033 0.033 0.900 M1= After “one unit” of evolution, the probability that an A mutates into a C is given by the corresponding entry in the matrix: p(A→C | d=1) = M1[A→C] = 0.033
  65. 65. http://gi.cebitec.uni-bielefeld.de/people/boecker/bilder/tree_of_life_new.gif
  66. 66. Augustin Augier, Arbre Botanique (1801)
  67. 67. Lamarck, Philosophie Zoologique , 1809
  68. 68. Darwin, Notebook B, 1837
  69. 69. Edward Hitchcock, Elementary Geology, 1840
  70. 70. Haeckel,The Evolution of Man, 1879
  71. 71. rRNA was used by Woese (1987) to group early life forms into three kingdoms
  72. 72. THEMA CENSY METKAMETJAMETMP METTHMETS3 METST ARCFU METHJ METMJ METLZ UNCMA METAC METMAMETBF METBU METTP HALWD NATPDHALMAHALSA PYRHOPYRABPYRFUPYRKO THEPD PYRCJPYRIL PYRAEPYRARSULSOSULAC SULTO STAMF AERPE HYPBU NANEQ PICTO THEACTHEVO RUBXD MYCPA MYCA1MYCUA MYCLE MYCBP MYCBO MYCTF MYCTU MYCTA MYCS2M YCSS M YCSK M YCSJM YCVP NO CFA RHO SR SACEN CO RG L CO RG B CO REF CO R D I C O R JK NO CSJ THEFY STRAW STRCO ACIC1 FRAAA FRASC CLAM 3 LEIXX ARTAT ARTS2 PROAC TROW T TROW 8 BIFLO BIFAA THET2 THET8DEIRA DEIGD RHOBA CHLMU CHLTR CHLTA CHLPN CHLCV CHLFF CHLAB PARUW LEPIN LEPIC LEPBL LEPBJCARRP MAGSM ERYLH NOVAD SPHAL ZYMMORHORT MAGMM GRABCGLUOX RHIMERHIL3 RHIEC AGRT5 RHILO MESSB BRUSUBRUMEBRUABBRUA2 BRUO2 BARHE BARQU BARBK BRAJABRASO BRASBRHOPA RHOP2 RHOPS RHOP5 RHOPB NITWN NITHX PARDP RHOS1RHOS4 JANSC SILPO SILST ROSDO HYPNA MARMM CAUCR PELUB WOLPM WOLTR EHRRW EHRRG EHRCJ EHRCR ANAPZ ANAMM NEOSM RICCN RICFE RICTY RICPR RICBR ORITB DICNV VESOH RUTMC LEGPA LEGPC LEGPH LEGPL COXBU PSYAR PSYCK ACIBT ACIAD WIGBR BUCBP BUCCC BUCAP BUCAI BLOPB BLOFL IDILO AERS4 AERHH ECOUT ECOK1 ECOL6 ECOL5 ECO57 ECOLI SHIDS SHIFL SHIF8 SHISS SHIBS SALTI SALCH SALTY SALPA PHO LL YERPE YER PA YER PN YER PP YER PS YER E8 ER W C TSO D G M BAUCH HAES1 PASM U HAEIN HAEIG HAEI8 HAEIE M ANSM ACTP2 HAEDU PSYINVIBVY VIBVUVIBPAVIBCHVIBF1PHOPR SHEAM SHELP SHEDOSHEFN SHEON SHESM SHESR SHESASHESW COLP3 PSEHT PSEA6 PSEAE PSEAB PSEPKPSEE4 PSEU2PSE14PSESMPSEF5PSEPF PSEU5 ALCBSMARAV HAHCHSACD2CHRSD THICR NITOCMETCAHALHLALHEH XYLFTXYLFAXANCP XANC8XANC5XANACXANOR XANOM NEIMFNEIMANEIMBNEIG1 CHRVOAZOSBAZOSE DECAR BORPEBORBRBORPA BORA1 RALEH RALEJRALMERALSO BURPSBURP1BURP0BURMA BURTA BURCM BURCABURCHBURS3 BURXLJANMA HERAR VEREI ACIAC ACISJ RHOFD POLNA POLSJ METPPTHIDA NITEU NITEC NITMU METFK FRATOFRATH FRATTFRAT1FRATWFRATN MYXXD ANADE DESPS DESVH DESVV DESDG LAWIP SYNFM SYNAS GEOSL GEOMG PELPD PELCD BDEBA CAMJJ CAMJR CAMJE CAMFF HELHP HELPY HELPH HELPJ HELAH WOLSU NITSB SULNB THIDN ACIBL SOLUE SALRD BACTN BACFR BACFN BACV8 PARD8 PORGI CYTH3 G RAFK FLAPJ CHLCH CHLPD PELLDCHLTE SYNP6 ANASP AN AVT TRIEISYNY3SYNELSYNJA SYNJBGLOVI PROM P PROM 5 PROM S PROM0 PROM9 PROMA PROM1 PROMTSYNPX SYNSCSYNS9 SYNPWSYNS3PROMM PROM3 SYNR3 GUITH ENCCU TRYBB LEIMALEIIN LEIBR OSTLU ORYSA ARATHPOPTR BOTCI MAGGR PHANO ASPFU YARLI ASHGO KLULA YEASTCANGA PICSTDEBHACANALLODEL SCHPO CRYNE USTMA APIME DROMEDROPSANOGA AEDAE CHICKORNAN LOXAF ECHTE DASNO MYOLU CANFAFELCA BOVIN TUPGB OTOGA HUMAN PANTR MACMU RABIT SPETR CAVPO MOUSERATNO ERIEU SORAR MONDOXENTR DANRE GASAC TETNG FUGRU ORYLA CIOSACIOIN CAEEL CAERE CAEBR DICDI CRYPV PLAF7 AQUAE TREPA TREDEBORGABORAP BORBU MOOTACARHZDESHYSYNWW FUSNN LACLALACLS LACLM STRPN STRR6 STRP2STRSV STRS2 STRSYSTRMU STRPD STRP1 STRP3 STRPG STRP8 STRP6 STRPM STRPC STRPB STRPF STRA5 STRA1 STRA3 STRT1 STRTD STRT2 ENTFA LEUM M O ENO B LACC3 LACSSLAC S1 PED PA LAC PL LACBA LACJO LACG A LACAC LACDB LACDA BACHD BACSK BACSU BACLD GEOKA GEOTN BACAN BACHK BACAH BACCZ BACC1 BACCR OCEIH LISMO LISMF LISIN LISW6 STAS1 STAHJ STAAR STAAM STAAN STAAW STAAS STAA3 STAAC STAA8 STAAB STAEQ STAES ONYPE AYWBP MESFL MYCMS MYCCT MYCPE UREPA MYCGE MYCPN MYCGA MYCH2MYCHJMYCH7 MYCMO MYCPU MYCS5 THETN CLOPECLOP1CLOPS CLONN CLOTE CLOABCLOD6CLOTH SYMTH DEHE1 DEHSC Archaea Bacteria Eukaryota Proteobacteria Actinobacteria Lactobacillales Bacilli Clostridia Cyanobacteria Tenericutes Spirochaetes Bacteroidetes Chlorobi Chlamydiae Chloroflexi Thermotogae Deinococcus-Thermus Acidobacteria Aquificae Verrucomicrobia Dictyoglomi candidate division TG1 Fusobacteria Planctomycetes
  73. 73. KLULA YEAST CANGA PICST DEBHA CANAL LODEL SCHPO CRYNE USTMA APIME DROME DROPS ANOGA AEDAE CHICK ORNAN LOXAF ECHTE DASNO MYOLU CANFA FELCA BOVIN TUPGB OTOGA HUM AN PANTR M ACM U RABIT SPETR C AVPO M O U SE R ATN O ERIEU SO RAR M O NDO XENTR D AN R E G ASAC TETN G FUG RU O R YLA CIO SA CIO IN CAEEL CAERE CAEBR DICDI CRYPV PLAF7 You are here.

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