Biochemistry 201 Advanced Molecular Biology Bioinformatics: Discovering Function from Sequence

Transkript

1 Biochemistry 201 Advanced Molecular Biology cmgm.stanford.edu/biochem201/ Bioinformatics: Discovering Function from Sequence Doug Brutlag Departments of Biochemistry March 6, 2000

2 Bioinformatics Text

3 Reviews

4 Durbin et al.

5 Central Paradigm of Molecular Biology DNA RNA Protein Phenotype (Symptoms) Molecules Structure Function Processes Mechanism Specificity Regulation

6 Central Paradigm of Bioinformatics Genetic Information Molecular Structure Biochemical Function Symptoms (Phenotype) SRAAINKHIVA VSYQTVSRVVN VSTATVSRALA GVTTTVSHVIN SGVSAVSAILN GVSEMTRRDLN TAYATIHVRVE GSQPTVSRELA MSIATITRGSN ISRETVGRILK FDISRLSHLFR LRPSRLAHLFR MTVETISRLLG TLEFHLHRLFK

7 Central Paradigm of Bioinformatics Genetic Information Molecular Structure Biochemical Function Symptoms (Phenotype) SRAAINKHIVA VSYQTVSRVVN VSTATVSRALA GVTTTVSHVIN SGVSAVSAILN GVSEMTRRDLN TAYATIHVRVE GSQPTVSRELA MSIATITRGSN ISRETVGRILK FDISRLSHLFR LRPSRLAHLFR MTVETISRLLG TLEFHLHRLFK

8 Discovering Function from Protein Sequence Sequences of Common Structure or Function Sequence Alignments VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS : : : : : : : : : : : 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN

9 Discovering Function from Protein Sequence Consensus Sequences Zinc Finger (C2H2 type) C.{2,4} C.{12} H.{3,5} H Sequences of Common Structure or Function Sequence Alignments VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS : : : : : : : : : : : 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN

10 Discovering Function from Protein Sequence BLOCK, Weight Matrix or Position Specific Scoring Matrix Position Consensus Sequences Zinc Finger (C2H2 type) C.{2,4} C.{12} H.{3,5} H A R N D C Q E G H I L K M F P S T W Y V Sequences of Common Structure or Function Sequence Alignments VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS : : : : : : : : : : : 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN

11 Discovering Function from Protein Sequence BLOCK, Weight Matrix or Position Specific Scoring Matrix Position A R N D C Q E G H I L K M F P S T W Y V Consensus Sequences Zinc Finger (C2H2 type) C.{2,4} C.{12} H.{3,5} H Sequences of Common Structure or Function Sequence Alignments VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS : : : : : : : : : : : 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN AA1 Profiles, PSI-BLAST Hidden Markov Models D 2 I 1 I 2 I 3 I 4 I 5 AA2 D 3 AA3 D 4 AA4 D 5 AA5 AA6

12 Data Mining calvinandhobbes.com/

13 Data Mining calvinandhobbes.com/

14 Data Mining calvinandhobbes.com/

15 Prosite Consensus Patterns htm Active site of trypsin-like serine proteases G D S G G Zinc Finger (C 2 H 2 type) C.{2,4} C.{12} H.{3,5} H Homeobox Domain Signature [LIVMF].{5} [LIVM].{4} [IV] [RKQ].. W.{8} [RK]

16 The Optimal Way to Develop Patterns

17 Generating Motifs from Aligned Protein Sequences TEAESNMNDPVAEYQQY TDARQDLYELEVDYANL TEARENIAVLERDFEEV TEAESNMNDLVSEYQQY TEVRANMNDLVAEYQQY SEAESNMNDLVSEYQQY TEAREDLAALEKDYEEV TEAREDLAALERDYIEV SEAREDLAALEKDYEEV AEAREDLAALEKDYIEV SEAREDLAALEKDYEEV SEAREDLAALERDYEEV

18 Generating Motifs from Aligned Protein Sequences TEAESNMNDPVAEYQQY TDARQDLYELEVDYANL TEARENIAVLERDFEEV TEAESNMNDLVSEYQQY TEVRANMNDLVAEYQQY SEAESNMNDLVSEYQQY TEAREDLAALEKDYEEV TEAREDLAALERDYIEV SEAREDLAALEKDYEEV AEAREDLAALEKDYIEV SEAREDLAALEKDYEEV SEAREDLAALERDYEEV TEARENIAVLERDFEEV SDVESDNNDPVAEYIQL A A LYE V ANY Q A S Q K

19 Generating Motifs from Aligned Protein Sequences TEAESNMNDPVAEYQQY TDARQDLYELEVDYANL TEARENIAVLERDFEEV TEAESNMNDLVSEYQQY TEVRANMNDLVAEYQQY SEAESNMNDLVSEYQQY TEAREDLAALEKDYEEV TEAREDLAALERDYIEV SEAREDLAALEKDYEEV AEAREDLAALEKDYIEV SEAREDLAALEKDYEEV SEAREDLAALERDYEEV TEAREDLAALERDYEEV S K I A

20 Generating Motifs from Aligned Protein Sequences TEAESNMNDPVAEYQQY TDARQDLYELEVDYANL TEARENIAVLERDFEEV TEAESNMNDLVSEYQQY TEVRANMNDLVAEYQQY SEAESNMNDLVSEYQQY TEAREDLAALEKDYEEV TEAREDLAALERDYIEV SEAREDLAALEKDYEEV AEAREDLAALEKDYIEV SEAREDLAALEKDYEEV SEAREDLAALERDYEEV TEARENIAVLERDFEEV SDVESDNNDPVAEYIQL A A LYE V ANY Q A S Q K

21 Amino Acid Substitution Groups Based on Physical Properties Only allow groups of amino acids sharing some chemical or physical property Group AG ST PAGST QN QNED KR VLI VLIM FYW KRH DE Property Tiny Hydroxyl Small Glutamine/Glutamate Acidic/Polar Strongly Basic Small hydrophobic Small hydrophobic Aromatic Basic Acidic

22 Allowable Amino Acid Substitution Groups FILMVY FILMV FILVY ILMV EKQR ILV FLY FWY KQR EKQ AST IV FY HY KR EQ DE DN ST AS M I V L F W Y H R K Q E D N T S A C G P

23 Finding emotifs

24 Histogram of Amino Acid Frequencies

25 Motif Dendrogram

26 emotifs Generated from the Helix-turn-helix Region of the LysR Family

27 PRINTS & Block Signatures INKHIQ VSRVVN ASRALM VSHVIN VSAILN IRRDLN THVRVE GSSELA MTRGSN VGRILK LSHLFR LAHLFR ISRLLG LHRLFK HSGEQLAETLGMSRAAINKHIQ VTLYDVAEYAGVSYQTVSRVVN AMIKDVALKAKVSTATVSRALM ATIKDVAKRAGVSTTTVSHVIN ITIYDLAELSGVSASAVSAILN LHLKDAAALLGVSEMTIRRDLN TAYAELAKQFGVSPGTIHVRVE GSLTEAAHLLGTSQPTVSRELA MSQRELKNELGAGIATITRGSN ITRQEIGQIVGCSRETVGRILK FDIASVAQHVCLSPSRLSHLFR LRIDEVARHVCLSPSRLAHLFR MTRGDIGNYLGLTVETISRLLG VTLEALADQVGMSPFHLHRLFK SRAAINKHIVA VSYQTVSRVVN VSTATVSRALA GVTTTVSHVIN SGVSAVSAILN GVSEMTRRDLN TAYATIHVRVE GSQPTVSRELA MSIATITRGSN ISRETVGRILK FDISRLSHLFR LRPSRLAHLFR MTVETISRLLG TLEFHLHRLFK Attwood, T. K., et al., (2000). PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Research, 28(1), Henikoff, J. G., Greene, E. A., Pietrokovski, S. and Henikoff, S. (2000). Increased coverage of protein families with the blocks database servers. Nucleic Acids Research, 28(1),

28 Identifying Protein Function with emotif

29 Identifying Protein Function with emotif Search

30 Mapping Sequence Motifs to Structural Motifs

31 3MOTIF Labeling

32 Sequence Redundancy in Prokaryotic Helix-Turn-Helix Motifs Sequence RCRO$LAMBD RCRO$BP434 RCRO$BPP22 RPC1$LAMBD RPC1$BP434 RPC1$BPP22 RPC2$LAMBD LACR$ECOLI CRP$ECOLI TRPR$ECOLI RPC1$CPP22 GALR$ECOLI Y77$BPT7 TER3$ECOLI VIVB$BPT7 DEOR$ECOLI RP32$BACSU Y28$BPT7 IMMRE$BPPH Helix Turn Helix F G Q T K T A K D L G V Y Q S A I N K A I H M T Q T E L A T K A G V K Q Q S I Q L I E A G T Q R A V A K A L G I S D A A V S Q W K E L S Q E S V A D K M G M G Q S G V G A L F N L N Q A E L A Q K V G T T Q Q S I E Q L E N I R Q A A L G K M V G V S N V A I S Q W E R L G T E K T A E A V G V D K S Q I S R W K R V T L Y D V A E Y A G V S Y Q T V S R V V N I T Q Q E I G Q I V G C S R E T V G R I L K M S Q R E L K N E L G A G I A T I T R G S N R G Q R K V A D A L G I N E S Q I S R W K G A T I K D V A R L A G V S V A T V S R V I N L S H R S L G E L Y G V S Q S T I T R I L Q L T T R K L A Q K L G V E Q P T L Y W H V K D Y Q A I F A Q Q L G G T Q S A A S Q I D E L H L K D A A A L L G V S E M T I R R D L N R T L E E V G K V F G V T R E R I R Q I E A E S N V S L A R T Y G V S Q Q T I C D I R K S T L E A V A G A L G I Q V S A I V G E E T

33 Position-Specific Scoring Matrices Position Structural or functional motif Examples of motif HSGEQLAETLGMSRAAINKHIQ VTLYDVAEYAGVSYQTVSRVVN AMIKDVALKAKVSTATVSRALM ATIKDVAKRAGVSTTTVSHVIN ITIYDLAELSGVSASAVSAILN LHLKDAAALLGVSEMTIRRDLN TAYAELAKQFGVSPGTIHVRVE GSLTEAAHLLGTSQPTVSRELA MSQRELKNELGAGIATITRGSN ITRQEIGQIVGCSRETVGRILK FDIASVAQHVCLSPSRLSHLFR LRIDEVARHVCLSPSRLAHLFR MTRGDIGNYLGLTVETISRLLG VTLEALADQVGMSPFHLHRLFK. A R N D C Q E G H I L K M F P S T W Y V

34 Block Signatures for a Protein Family (After Henikoff and Henikoff) INKHIQ VSRVVN ASRALM VSHVIN VSAILN IRRDLN THVRVE GSSELA MTRGSN VGRILK LSHLFR LAHLFR ISRLLG LHRLFK HSGEQLAETLGMSRAAINKHIQ VTLYDVAEYAGVSYQTVSRVVN AMIKDVALKAKVSTATVSRALM ATIKDVAKRAGVSTTTVSHVIN ITIYDLAELSGVSASAVSAILN LHLKDAAALLGVSEMTIRRDLN TAYAELAKQFGVSPGTIHVRVE GSLTEAAHLLGTSQPTVSRELA MSQRELKNELGAGIATITRGSN ITRQEIGQIVGCSRETVGRILK FDIASVAQHVCLSPSRLSHLFR LRIDEVARHVCLSPSRLAHLFR MTRGDIGNYLGLTVETISRLLG VTLEALADQVGMSPFHLHRLFK SRAAINKHIVA VSYQTVSRVVN VSTATVSRALA GVTTTVSHVIN SGVSAVSAILN GVSEMTRRDLN TAYATIHVRVE GSQPTVSRELA MSIATITRGSN ISRETVGRILK FDISRLSHLFR LRPSRLAHLFR MTVETISRLLG TLEFHLHRLFK

35 BLOCKS+ Is Based On Several Protein Family Databases PROSITE BlockMaker PRINTS BLOCKS Pfam ProDom BlockMaker DOMO BLOCKS+

36 ematrix Maker

37 An ematrix

38 ematrix Search (

39 ematrix Search Results ematrix-search/

40 ematrix & Similarity Search Identify 77% of Human Proteins

41 Sequence Alignment X X F--SGGNTHIYMNHVEQCKEILRREPKELCELVISGLPYKFRYLSTKE-QLK-Y : :: : : : : : ::::: :: GDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYN X X Region End Score = Similarity-weights - Penalties Region Start where: Region End Region Start Penalty = Gap-penalty + Size-of-gap x Gap-size-penalty

42 Smith-Waterman Similarity Search Query: HU-NS1 Maximal Score: 452 PAM Matrix: 200 Gap Penalty: 5 Gap Extension: 0.5 No. Score Match Length DB ID Description Expectation DBHB_ECOLI DNA-BINDING PROTEIN H 8.74e DBHB_SALTY DNA-BINDING PROTEIN H 1.54e DBHA_ECOLI DNA-BINDING PROTEIN H 1.64e DBHA_SALTY DNA-BINDING PROTEIN H 1.64e DBH_BACST DNA-BINDING PROTEIN I 1.35e DBH_BACSU DNA-BINDING PROTEIN I 1.35e DBH_VIBPR DNA-BINDING PROTEIN H 2.35e DBH_PSEAE DNA-BINDING PROTEIN H 2.14e DBH1_RHILE DNA-BINDING PROTEIN H 1.47e DBH_CLOPA DNA-BINDING PROTEIN H 2.52e DBH_RHIME DNA-BINDING PROTEIN H 3.18e DBH5_RHILE DNA-BINDING PROTEIN H 9.29e DBH_ANASP DNA-BINDING PROTEIN H 3.32e DBH_CRYPH DNA-BINDING PROTEIN H 2.70e DBH_THETH DNA-BINDING PROTEIN I 1.07e IHFA_SERMA INTEGRATION HOST FACT 4.46e IHFA_RHOCA INTEGRATION HOST FACT 3.52e IHFA_SALTY INTEGRATION HOST FACT 5.90e IHFA_ECOLI INTEGRATION HOST FACT 9.87e IHFB_ECOLI INTEGRATION HOST FACT 7.71e IHFB_SERMA INTEGRATION HOST FACT 7.71e TF1_BPSP1 TRANSCRIPTION FACTOR 3.42e DBH_THEAC DNA-BINDING PROTEIN H 2.12e GLGA_ECOLI GLYCOGEN SYNTHASE (EC 3.80e-01

43 Original BLAST Algorithm Indexes database Starts with all overlapping words from query Calculates neighborhood of each word using BLOSUM matrix and probability threshold Looks up all words and neighbors from query in database index Extends High-Scoring Segment Pairs (HSPs( HSPs) ) left and right to maximal length Finds Maximal Segment Pairs (MSPs( MSPs) ) between query and database Does not permit gaps in alignments

44 GAPPED BLAST Starts with a Two Hit Approach

45 GAPPED BLAST Extension of Two Hit HSP

46 GAPPED BLAST Alignment

47 Extreme Value Distribution of Scores

48 Expectation of High Scoring Segment Pairs (HSPs( HSPs) Pr ob(s > X) 1 exp{ Ke X } where r r i =1 j =1 is the root of the equation: p i p j exp { s ij } = 1 p i and p j are the probabilities of each residue in each sequence, s ij are the similarity scores of two residues. If the expected value of the scores for random sequences is < 0, i. e. r r p i p j s ij < 0 i =1 j =1 then there are two solutions for, zero and one other positive root Distribution of Scores > S Score S

49 Decypher Database Search Engine decypher.stanford.edu/

50 Decypher Database Search Engine decypher.stanford.edu/

51 Profiles & Hidden Markov Models D 2 D 3 D 4 D 5 I 1 I 2 I 3 I 4 I 5 AA1 AA2 AA3 AA4 AA5 AA6

52 Discovering Function from Protein Sequence BLOCK, Weight Matrix or Position Specific Scoring Matrix Position A R N D C Q E G H I L K M F P S T W Y V Consensus Sequences Zinc Finger (C2H2 type) C.{2,4} C.{12} H.{3,5} H Sequences of Common Structure or Function Sequence Alignments VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGS : : : : : : : : : : : 2 HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGN AA1 Profiles, PSI-BLAST Hidden Markov Models D 2 I 1 I 2 I 3 I 4 I 5 AA2 D 3 AA3 D 4 AA4 D 5 AA5 AA6

53 DoubleTwist s Home Page

54 What is DoubleTwist.com? DoubleTwist is a web portal for life sciences DoubleTwist accepts sequence & text queries DoubleTwist provides multiple analyses DNA & protein sequence databases Completed genome database Clustered EST databases Motif & domain databases DoubleTwist provides research reports DoubleTwist provides evaluation of results DoubleTwist links to reagents, clones & protocols DoubleTwist is agent driven DoubleTwist runs daily

55 Query Sequences

56 DoubleTwist Research Agents Given an EST, cdna, genomic DNA or protein sequence DoubleTwist will: Find identical cdna, EST or genomic sequences Find similar cdna, EST or genomic sequences Find identical protein coding regions Find coding regions for similar proteins Find functional motifs in coding regions Find similar proteins whose structure is known Find similar sequences that have been patented

57 Assigning DoubleTwist Agents to Queries

58 Assigning DoubleTwist Agents to Queries

59 How one DoubleTwist Agent Works Agent name: Find Similar ESTs Initial steps 1. Remove trailing poly(a) and poly(t) 2. Mask vector sequences 3. Mask repetitive/low complexity regions Every night Run BLAST2N against GenBank nightly updates Return hits that fall within acceptable parameters determine if hit is an EST from specified tissue/organism Notify user via (Web Link points to Report) flag hits with confidence values (high/medium/low)

60 DoubleTwist Protein Query versus EST Similarity Agent

61 DoubleTwist s Databases Sequence/motif databases DoubleTwist curated databases SwissProt Human EST cluster database TREMBL Mouse EST cluster database dbest Arabidopsis EST cluster database PDB Completed Genomes Database PIR Comprehensive Vector Database BLOCKS+ PRODOM Other databases in development PRINTS AlphaGene clone database PFAM ClonTech clones & reagents UNIGENE ProNet (Myriad Genetics) CGAP Microbial metabolic database (Karp) Patent Database Many others Repbase GenBank non-redundant nucleotide database GenBank non-redundant protein database GenBank daily DNA database updates GenBank daily protein database updates

62 DoubleTwist s Algorithms BLAST2N (NCBI) BLAST2X (NCBI) TBLAST2N (NCBI) TBLAST2X (NCBI) MASK (vector masking, DoubleTwist Inc.) RepeatMasker (Smit & Green, U. Washington) Blocks Search (Henikoff & Henikoff, FHCRC) GRAIL (Uberbacher et al.,doe) GenScan (Burge et al., Stanford & MIT) HalfWise (Birney et al., Sanger Center) HMMer (Eddy & Sonnhammer, Wash U. & MRC) SIM4 (Miller et al., Penn State)

63 Advantages of DoubleTwist s Clustered EST Databases Clustering and alignment tool (CAT) detects alternative splicing and sequence polymorphisms CAT corrects cloning & sequencing errors CAT removes insertion/deletion errors resulting in longer open reading frames (ORFs) CAT distinguishes alternative splicing from sequencing artifacts (chimeras & lane tracking errors) CAT distinguishes SNPs from sequencing errors Better drug target discovery Increased sensitivity (target discovery) Improved selectivity (target validation)

64 DoubleTwist Clusters Resolve Alternative Splicing

65 Single Nucleotide Polymorphisms: Resolving Adjacent Polymorphic Sites A WIAF-1302 GTCTTCAGCCTCCTCTACCCTACGAGATCTGGAGCAACAGCTAGGAAA ^ [A/G] GTTTTCAGCCTCCTCTACCCTACATGATCTGGAGCAA gene_gnl UG Hs#S576 GTTTTCAGCCTCCTCTACCCTACATGATCTGGAGCAA AA GTTTTCAGCCTCCTCTACCCTACATGATCTGGAGCAA R.C.T40995 GTCTTCAGCCTCCTCTACCCTACATGATCTGGAGCAA gene_gnl UG Hs#S1790 GTCTTCAGCCTCCTCTACCCTACATGATCTGGAGCAA gene_gnl UG Hs#S5761 GTCTTCAGCCTCCTCTACCCTACGAGATCTGGAGCAA gene_gnl UG Hs#S4384 GTCTTCAGCCTCCTCTACCCTACGAGATCTGGAGCAA genel UG Hs#S GTCTTCAGCCTCCTCTACCCTACGAGATCTGGAGCAA gene_gnl UG Hs#S1791 GTCTTCAGCCTCCTCTACCCTACAAGATCTGGAGCAA gene_gnl UG Hs#S GTCTTCAGCCTCCTCTACGCTACAAGATCTGGAGCAA AA GTCTTCAGCCTACTATACCCTACAAGATCTGGCGCAA R.C.AI GTCTTCAGCCTCCTCTACCCTACCAGATCTGGAGCAA AA GTCTTCAGCCTCCTCTACCCTACAAGATCTGGAGCAA D57354 GTCTTCAGCCTCCTCTACCCTACAAGATCTGGAGCAA AA ^ [C/T] ^^ [A/T] [A/G]

66 DoubleTwist s View of an EST Cluster

67 DoubleTwist Research Reports

68 A DoubleTwist Research Report: Protein Function

69 A DoubleTwist Research Report: Protein Functional Motifs

70 A DoubleTwist Research Report Late Breaking Database Entries

71 Patent, Structure and EST Reports

72 Viewing Monitor Agent Reports

73 Notification of New Findings Date: Friday, 4 Feb :18: (PST) From: report <report@doubletwist.com> To: BRUTLAG <brutlag@stanford.edu> Subject: Find Similar Proteins This mail is auto-generated, and was triggered by NEW FINDINGS for the sequence you specified at: Here is the outline: Agent: Find Similar Proteins Sequence: MSH-2 Details: The links above are secured by password, and all access to DoubleTwist is monitored to ensure privacy. For more information about DoubleTwist, security and privacy, please go to:

74 Similar Protein Monitor Agent Report

75 Submission Date for CAA21156

76 Similar Protein Monitor Agent Report

77 DoubleTwist Genome Viewer

78 PSI-BLAST In Brief 1) Compare the query sequence to database 2) Construct profile from significant similarities 3) Compare the profile to database 4) Repeat step 2 and 3 until convergence

79 PSI-BLAST Results Contain Multiple Similar Regions Major Steps: 1) Clustering 2) Alignment 3) Trimming

80 Clusters Are Organized Into Groups 8 2 9

81 eblocks Summary SWISS-PROT 79,449 Sequences Filtered Target Set 57,266 Sequences PSI-BLAST Searches 17,415 Final Number Of Groups 16,658 Final Number Of Blocks 74,396

82 eblocks Is More Comprehensive 38% 78% BLOCKS+ (9,498) eblocks (74,396)

83 Web Access to eblocks ( edu/)

84 An Entry From eblocks

85 An Entry From eblocks

86 A Sample Keyword Search

87 Search A Sequence