1 Mona Singh

What is computational biology?

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Genome

• The entire hereditary information content of an organism

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DNA

• String over 4 letter alphabet A, T, G, C

• Organism’s genome is distributed over chromosomes (e.g., 46 chromosomes in human—22 pairs & XY)

• Genome size: number of base pairs in an organism

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Genome SizesHuman 3 billion bps

Mouse 3 billion bps

Fruit fly 165 million bps

Nematode worm

97 million bps

Yeast 15 million bps

E coli 5 million bps

~ 400 genomes sequenced

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How are genomes sequenced?

• Can only sequence a few hundred base pairs at a time

• Make many copies of the DNA and cut into smaller (overlapping) pieces

• Assemble pieces: certain substrings occur in multiple fragments

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Genomes to Life

ATGCCTTACGTACCCTGCGGCAGCACT

?Genome

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• Portions of DNA code for genes, which carry the information for making proteins

• Proteins play key roles in most biological processes (e.g., signaling, catalysis, immune response, etc.)

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gucgcuaccauuaccaguuggucuggugucaaaaauaauaauaaccgggcaggccaugucugcccguauuucgcguaaggaaauccauuauguacuauuuaaaaaacacaaacuuuuggauguucgguuuauucuuuuucuuuuacuuuuuuaucaugggagccuacuucccguuuuucccgauuuggcuacaugacaucaaccauaucagcaaaagugauacggguauuauuuuugccgcuauuucucuguucucgcuauuauuccaaccgcuguuuggucugcuuucugacaaacucgggcugcgcaaauaccugcuguggauuauuaccggcauguuagugauguuugcgccguucuuuauuuuuaucuucgggccacuguuacaauacaacauuuuaguaggaucgauuguuggugguauuuaucuaggcuuuuguuuuaacgccggugcgccagcaguagaggcauuuauugagaaagucagccgucgcaguaauuucgaauuuggucgcgcgcggauguuuggcuguguuggcugggcgcugugugccucgauugucggcaucauguucaccaucaauaaucaguuuguuuucuggcugggcucuggcugugcacucauccucgccguuuuacucuuuuucgccaaaacggaugcgcccucuucugccacgguugccaaugcgguaggugccaaccauucggcauuuagccuuaagcuggcacuggaacuguucagacagccaaaacugugguuuuugucacuguauguuauuggcguuuccugcaccuacgauGuuuuugaccaacaguuugcuaauuucuuuacuucguucugucaggugaa...gcaaucaaugucggaugcggcgcgacgcu

Gene Finding

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gucgcuaccauuaccaguuggucuggugucaaaaauaauaauaaccgggcaggccaugucugcccguauuucgcguaaggaaauccauuauguacuauuuaaaaaacacaaacuuuuggauguucgguuuauucuuuuucuuuuacuuuuuuaucaugggagccuacuucccguuuuucccgauuuggcuacaugacaucaaccauaucagcaaaagugauacggguauuauuuuugccgcuauuucucuguucucgcuauuauuccaaccgcuguuuggucugcuuucugacaaacucgggcugcgcaaauaccugcuguggauuauuaccggcauguuagugauguuugcgccguucuuuauuuuuaucuucgggccacuguuacaauacaacauuuuaguaggaucgauuguuggugguauuuaucuaggcuuuuguuuuaacgccggugcgccagcaguagaggcauuuauugagaaagucagccgucgcaguaauuucgaauuuggucgcgcgcggauguuuggcuguguuggcugggcgcugugugccucgauugucggcaucauguucaccaucaauaaucaguuuguuuucuggcugggcucuggcugugcacucauccucgccguuuuacucuuuuucgccaaaacggaugcgcccucuucugccacgguugccaaugcgguaggugccaaccauucggcauuuagccuuaagcuggcacuggaacuguucagacagccaaaacugugguuuuugucacuguauguuauuggcguuuccugcaccuacgauGuuuuugaccaacaguuugcuaauuucuuuacuucguucugucaggugaa...gcaaucaaugucggaugcggcgcgacgcu

MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT

Gene Finding

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AUG = methionine/startUUA = LeucineUUG = Leucine

UAA = StopUAG = StopUGA = Stop...

The Genetic Code

Stryer, Biochemistry

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Gene Findinggucgcuaccauuaccaguuggucuggugucaaaaauaauaauaaccgggcaggccaugucugcccguauuucgcguaaggaaauccauuauguacuauuuaaaaaacacaaacuuuuggauguucgguuuauucuuuuucuuuuacuuuuuuaucaugggagccuacuucccguuuuucccgauuuggcuacaugacaucaaccauaucagcaaaagugauacggguauuauuuuugccgcuauuucucuguucucgcuauuauuccaaccgcuguuuggucugcuuucugacaaacucgggcugcgcaaauaccugcuguggauuauuaccggcauguuagugauguuugcgccguucuuuauuuuuaucuucgggccacuguuacaauacaacauuuuaguaggaucgauuguuggugguauuuaucuaggcuuuuguuuuaacgccggugcgccagcaguagaggcauuuauugagaaagucagccgucgcaguaauuucgaauuuggucgcgcgcggauguuuggcuguguuggcugggcgcugugugccucgauugucggcaucauguucaccaucaauaaucaguuuguuuucuggcugggcucuggcugugcacucauccucgccguuuuacucuuuuucgccaaaacggaugcgcccucuucugccacgguugccaaugcgguaggugccaaccauucggcauuuagccuuaagcuggcacuggaacuguucagacagccaaaacugugguuuuugucacuguauguuauuggcguuuccugcaccuacgauguuuuugaccaacaguuugcuaauuucuuuacuucguucugucaggugaa...gcaaucaaugucggaugcggcgcgacgcu

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Gene Findingaug ucu gcc cgu auu ucg cgu aag gaa auc cau uau gua cua uuu aaa ...

Met Ser Ala Arg Ile Ser Arg Lys Glu Ile His Tyr Val Leu Phe Lys ...

M S A R I S R K E I H Y V L F K ...

Reading offfrom 1st starttriplet

Translating(3 letter aminoacid code)

(1 letter code)

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Gene Findingaug ucu gcc cgu auu ucg cgu aag gaa auc cau uau gua cua uuu aaa ...

Met Ser Ala Arg Ile Ser Arg Lys Glu Ile His Tyr Val Leu Phe Lys ...

M S A R I S R K E I H Y V L F K ...

Reading offfrom 1st starttriplet

Translating(3 letter aminoacid code)

(1 letter code)

M Y Y L K N T N F W M F G L F F ...Actual protein sequence

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Computational Gene Finding Methods

• Statistical bias: protein coding regions “look different”

- compare coding vs. non-coding regions (Hidden Markov Models, Neural Nets)• Sequence similarity - similar to known protein?

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Gene finding is hard

• In some genomes, only a small portion of genome codes for protein (needle in haystack)

• Some genes contain introns and exons – exons are the part that actually encode the protein part – and exons can be short

• Have to get the precise boundaries to get correct protein

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Number of genesHuman ~30,000

Mouse ~30,000

Fruit fly ~13,500

Nematode worm

~19,000

Yeast ~6,000

E coli ~4,000

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MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYIT

Predicting Protein Function

DNA binding protein

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Functions of Human Proteins

Science, 2001

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Sequence similarity

CF: EGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLL-----NT: QAAQPLVHGVSLTLQRGRVLALVGGSGSGKSLTCAATLGILPAGVR

CF: NTEGEIQIDGVSWDSITL---------QQWRKAFGVIPQKVFIFSGNT: QTAGEILADGKPVSPCALRGIKIATIMQNPRSAFNPL---------

CF: TFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQFP-GKLDFVLVDGGNT: ---HTMHTHARETCLALGKPADDATLTAAIEAVGLENAARVLKLYP

CF: CVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPV NT: FEMSGGMLQRMMIAMAVLCESPFIIADEPTTDLDVV

Ex: cystic fibrosis gene and bacterial nickel transport gene

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Database Searches

http://www.ncbi.nlm.nih.gov

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Database SearchesSequences producing significant alignments: E-Value

gi|5523990|gb|AAD44047.1|AF108138_1 (AF108138) DNA helicase 4e-84gi|7511524|pir||T37310 PIF1 protein - Caenorhabditis elegans helicase 1e-77gi|7493349|pir||T40739 rrm3-pif1 helicase homolog - fission... 3e-59gi|11282390|pir||T47241 RRM3/PIF1 helicase homolog - fission yeast 3e-59gi|6321820|ref|NP_011896.1| DNA helicase; Rrm3p [Saccharomyces 4e-43gi|6323579|ref|NP_013650.1| 5' to 3' DNA helicase; Pif1p [Saccharo 1e-41gi|558414|emb|CAA86260.1| (Z38114) len: 750, CAI: 0.14, inc... 1e-41gi|7687929|emb|CAB89609.1| (AL354532) possible DNA helicase... 4e-41

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Protein Structure

Sequence: KETAAAKFERQHMDSSTSAASSSN…Structure:

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Primary TertiarySecondary Quaternary

Amino acids helixPolypeptide

chainAssembledsubunits

Proteins

Lehninger, Principles of Biochemistry

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Protein Structure Prediction

•Physics-based methods•Statistics-based method

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Statistics & Protein Structure Prediction

Given a new sequence and a library of folds, figure out which (if any) is a good fit to the sequence.

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Secondary structure prediction

• Given a protein sequence, can you tell its secondary structure– E.g., LKVVAKRELVQNNQ aaaa bbbb aaaaaaa

a=alpha, b=beta : ~70% accuracy(neural nets or other learning techniques)

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Genome annotation

• Many other important features of DNA– E.g., proteins bind DNA regulatory

elements: determines which genes are “on” when

• Statistical & comparative approaches for finding them– Motif finding

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Prokaryotes Eukaryotes

Universal phylogenetic tree

Woese et al.

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Building phylogenetic trees

Use DNA (or protein) sequences from various organisms

e.g., human ATCGAGGC mouse ATCCAGCC yeast ATTAAGTA

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Building phylogenetic trees

Human Mouse

Yeast

Human

0 2 4

Mouse 2 0 4

Yeast 4 4 0

E.g.,DistanceMatrix:

Tree:1 1

1 2

Human Mouse Yeast

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DNA RNA

Protein

Stimulus

Sti

mu

lus

Intracellular networks

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DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

Network of cells

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DNA RNA

Protein

fn

fn

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Lecture Notes

• www.cs.princeton.edu/~mona/computational_biology_notes.html