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Doug Brutlag 2011 Bioinformatics Genomics, Bioinformatics.

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1 Doug Brutlag 2011 Bioinformatics http://biochem158.stanford.edu/bioinformatics.html http://biochem158.stanford.edu/bioinformatics.html Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/ Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine

2 Doug Brutlag 2011 Human Biology 40 th Birthday Friday, October 21, 2011 Friday, October 21, 2011

3 Doug Brutlag 2011 What is Bioinformatics? RNAProtein DNAPhenotype SelectionEvolution Individuals Populations Biological Information

4 Doug Brutlag 2011 Computational Goals of Bioinformatics Learn & Generalize: Discover conserved patterns (models) of sequences, structures, metabolism & chemistries from well-studied examples. Prediction: Infer function or structure of newly sequenced genes, genomes, proteomes or proteins from these generalizations. Organize & Integrate: Develop a systematic and genomic approach to molecular interactions, metabolism, cell signaling, gene expression… Basis of systems biology Simulate: Model gene expression, gene regulation, protein folding, protein-protein interaction, protein-ligand binding, catalytic function, metabolism… Goal of systems biology. Engineer: Construct novel organisms or novel functions or novel regulation of genes and proteins. Basis of synthetic biology. Target: Mutations, RNAi to specific genes and transcripts or drugs to specific protein targets. Practical biological and medical use of bioinformatics.

5 Doug Brutlag 2011 Central Paradigm of Molecular Biology DNARNAProtein Phenotype

6 Doug Brutlag 2011 MVHLTPEEKT AVNALWGKVN VDAVGGEALG RLLVVYPWTQ RFFESFGDLS SPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFSQLS ELHCDKLHVD PENFRLLGNV LVCVLARNFG KEFTPQMQAA YQKVVAGVAN ALAHKYH Genetic Information Central Paradigm of Bioinformatics Phenotype (Symptoms) Biochemical Function Molecular Structure

7 Doug Brutlag 2011 Central Paradigm of Bioinformatics Molecular Structure Phenotype (Symptoms) Biochemical Function Genetic Information MVHLTPEEKT AVNALWGKVN VDAVGGEALG RLLVVYPWTQ RFFESFGDLS SPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFSQLS ELHCDKLHVD PENFRLLGNV LVCVLARNFG KEFTPQMQAA YQKVVAGVAN ALAHKYH

8 Doug Brutlag 2011 Challenges Understanding Genetic Information Genetic Information Molecular Structure Biochemical Function Phenotype Genetic information is redundant Structural information is redundant

9 Doug Brutlag 2011 Soybean Leghemoglobin and Sperm Whale Myoglobin Soybean LeghemoglobinSperm Whale Myoglobin

10 Doug Brutlag 2011 Challenges Understanding Genetic Information Genetic Information Molecular Structure Biochemical Function Phenotype Genetic information is redundant Structural information is redundant Genes and proteins are meta-stable

11 Doug Brutlag 2011 Challenges Understanding Genetic Information Genetic Information Molecular Structure Biochemical Function Phenotype Genetic information is redundant Structural information is redundant Genes and proteins are meta-stable Genes and proteins are one dimensional but their function depends on three-dimensional structure

12 Doug Brutlag 2011 Discovering Function from Protein Sequence Sequence Similarity 10 20 30 40 50 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS |:| :|: | |:|||| | |:||| |: : :|:| :| | |: | 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN 10 20 30 40 50 Sequences of Common Structure or Function

13 Doug Brutlag 2011 Dayhoff’s PAM 250 Amino Acid Replacement Matrix (1978)

14 Doug Brutlag 2011 Discovering Function from Protein Sequence Consensus Sequences or Sequence Motifs Zinc Finger (C2H2 type) C X{2,4} C X{12} H X{3,5} H Sequence Similarity 10 20 30 40 50 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS |:| :|: | |:|||| | |:||| |: : :|:| :| | |: | 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN 10 20 30 40 50 Sequences of Common Structure or Function

15 Doug Brutlag 2011 A Typical Motif: Zinc Finger DNA Binding Motif C..C............H....H

16 Doug Brutlag 2011Position 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12 A 2 1 3 13 10 12 67 4 13 9 1 2 2 1 3 13 10 12 67 4 13 9 1 2 R 7 5 8 9 4 0 1 16 7 0 1 0 7 5 8 9 4 0 1 16 7 0 1 0 N 0 8 0 1 0 0 0 2 1 1 10 0 0 8 0 1 0 0 0 2 1 1 10 0 D 0 1 0 1 13 0 0 12 1 0 4 0 0 1 0 1 13 0 0 12 1 0 4 0 C 0 0 1 0 0 0 0 0 0 2 2 1 0 0 1 0 0 0 0 0 0 2 2 1 Q 1 1 21 8 10 0 0 7 6 0 0 2 1 1 21 8 10 0 0 7 6 0 0 2 E 2 0 0 9 21 0 0 15 7 3 3 0 2 0 0 9 21 0 0 15 7 3 3 0 G 9 7 1 4 0 0 8 0 0 0 46 0 9 7 1 4 0 0 8 0 0 0 46 0 H 4 3 1 1 2 0 0 2 2 0 5 0 4 3 1 1 2 0 0 2 2 0 5 0 I 10 0 11 1 2 10 0 4 9 3 0 16 10 0 11 1 2 10 0 4 9 3 0 16 L 16 1 17 0 1 31 0 3 11 24 0 14 16 1 17 0 1 31 0 3 11 24 0 14 K 3 4 5 10 11 1 1 13 10 0 5 2 3 4 5 10 11 1 1 13 10 0 5 2 M 7 1 1 0 0 0 0 0 5 7 1 8 7 1 1 0 0 0 0 0 5 7 1 8 F 4 0 3 0 0 4 0 0 0 10 0 0 4 0 3 0 0 4 0 0 0 10 0 0 P 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 S 1 17 0 8 3 1 3 0 2 2 2 0 1 17 0 8 3 1 3 0 2 2 2 0 T 5 22 3 11 1 5 0 2 2 2 0 5 5 22 3 11 1 5 0 2 2 2 0 5 W 2 0 0 0 0 0 0 0 0 1 0 1 2 0 0 0 0 0 0 0 0 1 0 1 Y 1 0 4 2 0 1 0 0 2 4 0 1 1 0 4 2 0 1 0 0 2 4 0 1 V 6 3 1 1 2 15 0 0 2 12 0 28 6 3 1 1 2 15 0 0 2 12 0 28 BLOCKs, PRINTs, PSSMS or Weight Matrices Discovering Function from Protein Sequence Consensus Sequences or Sequence Motifs Zinc Finger (C2H2 type) C X{2,4} C X{12} H X{3,5} H Sequence Similarity 10 20 30 40 50 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS |:| :|: | |:|||| | |:||| |: : :|:| :| | |: | 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN 10 20 30 40 50 Sequences of Common Structure or Function

17 Doug Brutlag 2011 Position-Specific Scoring Matrix for Prokaryotic Helix-Turn-Helix Motifs SequenceHelix TurnHelix RCRO_LAMBDF G Q T K T A K D L G V Y Q S A I N K A I H RCRO_BP434M T Q T E L A T K A G V K Q Q S I Q L I E A RCRO_BPP22G T Q R A V A K A L G I S D A A V S Q W K E RPC1_LAMBDL S Q E S V A D K M G M G Q S G V G A L F N RPC1_BP434L N Q A E L A Q K V G T T Q Q S I E Q L E N RPC1_BPP22I R Q A A L G K M V G V S N V A I S Q W E R RPC2_LAMBDL G T E K T A E A V G V D K S Q I S R W K R LACR_ECOLIV T L Y D V A E Y A G V S Y Q T V S R V V N CRP_ECOLII T Q Q E I G Q I V G C S R E T V G R I L K TRPR_ECOLIM S Q R E L K N E L G A G I A T I T R G S N RPC1_CPP22R G Q R K V A D A L G I N E S Q I S R W K G GALR_ECOLIA T I K D V A R L A G V S V A T V S R V I N Y77_BPT7L S H R S L G E L Y G V S Q S T I T R I L Q TER3_ECOLIL T T R K L A Q K L G V E Q P T L Y W H V K VIVB_BPT7D Y Q A I F A Q Q L G G T Q S A A S Q I D E DEOR_ECOLIL H L K D A A A L L G V S E M T I R R D L N RP32_BACSUR T L E E V G K V F G V T R E R I R Q I E A Y28_BPT7E S N V S L A R T Y G V S Q Q T I C D I R K IMMRE_BPPHS T L E A V A G A L G I Q V S A I V G E E T

18 Doug Brutlag 2011 Profiles, PSI-BLAST Hidden Markov Models AA1AA2AA3AA4AA5AA6 I 1 I 2 I 3 I 4 I 5 D 2 D 3 D 4 D 5 Discovering Function from Protein Sequence Position 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 9 10 11 12 A 2 1 3 13 10 12 67 4 13 9 1 2 2 1 3 13 10 12 67 4 13 9 1 2 R 7 5 8 9 4 0 1 16 7 0 1 0 7 5 8 9 4 0 1 16 7 0 1 0 N 0 8 0 1 0 0 0 2 1 1 10 0 0 8 0 1 0 0 0 2 1 1 10 0 D 0 1 0 1 13 0 0 12 1 0 4 0 0 1 0 1 13 0 0 12 1 0 4 0 C 0 0 1 0 0 0 0 0 0 2 2 1 0 0 1 0 0 0 0 0 0 2 2 1 Q 1 1 21 8 10 0 0 7 6 0 0 2 1 1 21 8 10 0 0 7 6 0 0 2 E 2 0 0 9 21 0 0 15 7 3 3 0 2 0 0 9 21 0 0 15 7 3 3 0 G 9 7 1 4 0 0 8 0 0 0 46 0 9 7 1 4 0 0 8 0 0 0 46 0 H 4 3 1 1 2 0 0 2 2 0 5 0 4 3 1 1 2 0 0 2 2 0 5 0 I 10 0 11 1 2 10 0 4 9 3 0 16 10 0 11 1 2 10 0 4 9 3 0 16 L 16 1 17 0 1 31 0 3 11 24 0 14 16 1 17 0 1 31 0 3 11 24 0 14 K 3 4 5 10 11 1 1 13 10 0 5 2 3 4 5 10 11 1 1 13 10 0 5 2 M 7 1 1 0 0 0 0 0 5 7 1 8 7 1 1 0 0 0 0 0 5 7 1 8 F 4 0 3 0 0 4 0 0 0 10 0 0 4 0 3 0 0 4 0 0 0 10 0 0 P 0 6 0 1 0 0 0 0 0 0 0 0 0 6 0 1 0 0 0 0 0 0 0 0 S 1 17 0 8 3 1 3 0 2 2 2 0 1 17 0 8 3 1 3 0 2 2 2 0 T 5 22 3 11 1 5 0 2 2 2 0 5 5 22 3 11 1 5 0 2 2 2 0 5 W 2 0 0 0 0 0 0 0 0 1 0 1 2 0 0 0 0 0 0 0 0 1 0 1 Y 1 0 4 2 0 1 0 0 2 4 0 1 1 0 4 2 0 1 0 0 2 4 0 1 V 6 3 1 1 2 15 0 0 2 12 0 28 6 3 1 1 2 15 0 0 2 12 0 28 BLOCKs, PRINTs, PSSMS or Weight Matrices Consensus Sequences or Sequence Motifs Zinc Finger (C2H2 type) C X{2,4} C X{12} H X{3,5} H Sequence Similarity 10 20 30 40 50 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS |:| :|: | |:|||| | |:||| |: : :|:| :| | |: | 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN 10 20 30 40 50 Sequences of Common Structure or Function

19 Doug Brutlag 2011 Data Mining: The Seach for Buried Treasure

20 Doug Brutlag 2011 Data Mining: The Seach for Buried Treasure

21 Doug Brutlag 2011 Data Mining: The Seach for Buried Treasure

22 Doug Brutlag 2011 PROSITE Patterns http://expasy.org/prosite/ http://expasy.org/prosite/ Active site of trypsin-like serine proteases G D S G G Zinc Finger (C 2 H 2 type) C-X(2,4)-C-X(12)-H-X(3,5)-H N-Glycosylation Site N-[^P]-[S T]-[^P] Homeobox Domain Signature [LIVMF]-X(5)-[LIVM]-X(4)-[IV]-[RKQ]-X-W-X(8)-[RK]

23 Doug Brutlag 2011 Swiss Institute of Bioinformatics http://www.isb-sib.ch/ http://www.isb-sib.ch/

24 Doug Brutlag 2011 Expasy Bioinformatics Resource Portal http://expasy.org/ http://expasy.org/

25 Doug Brutlag 2011 Expasy Bioinformatics Resource Portal http://expasy.org/ http://expasy.org/

26 Doug Brutlag 2011 Prosite Database http://prosite.expasy.org/ http://prosite.expasy.org/

27 Doug Brutlag 2011 UniProt Knowledge Base http://www.uniprot.org/ http://www.uniprot.org/

28 Doug Brutlag 2011 UniProt Opsin Entries http://www.uniprot.org/uniprot/?query=opsin&sort=score http://www.uniprot.org/uniprot/?query=opsin&sort=score

29 Doug Brutlag 2011 UniProt Homo sapiens Opsin Entries http://www.uniprot.org/uniprot/?query=opsin+AND+organism%3A%22homo+sapiens%22&sort=score http://www.uniprot.org/uniprot/?query=opsin+AND+organism%3A%22homo+sapiens%22&sort=score

30 Doug Brutlag 2011 UniProt Homo sapiens OPN1MW Entry http://www.uniprot.org/uniprot/P04001 http://www.uniprot.org/uniprot/P04001

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