麻省理工大学：《Foundations of Biology》课程教学资源（英文版）Lecture 3 More Multiple Sequence Alignment

791- Lecture #3 Michael Yaffe More Multiple Sequence Alignment and Motif Scanning, Database Searching R 0导中o998:求8 Computed _iing f and mmkelago(Schneider Stephe ns, 199o

7.91 – Lecture #3 More Multiple Sequence Alignment -and￾Motif Scanning, Database Searching Michael Yaffe

Outline Multiple Sequence Alignment -Carillo Lipman Clustal(W Position-Specific Scoring Matrices(PSSM) Information content, Shannon entropy Sequence logos Hidden markov models Other approaches: Genetic algorithms expectation maximization MEME, Gibbs sampler FASTA, Blast searching, Smith-Waterman ·Psi- Blast Reading- Mount p.139-150,152157,161-171,185-198

Outline • Multiple Sequence Alignment - Carillo & Lipman, Clustal(W) • Position-Specific Scoring Matrices (PSSM) • Information content, Shannon entropy • Sequence logos • Hidden Markov Models • …Other approaches: Genetic algorithms, expectation maximization, MEME,Gibbs sampler • FASTA, Blast searching, Smith-Waterman • Psi-Blast Reading - Mount p. 139-150, 152-157, 161-171, 185-198

Multiple Sequence Alignments Sequences are aligned so as to bring the greatest number of single characters into register If we include gaps, mismatches then even dynamic programming becomes limited to 3 sequences unless they are very short.. need an alternative approach Why?

Multiple Sequence Alignments • Sequences are aligned so as to bring the greatest number of single characters into register. • If we include gaps, mismatches, then even dynamic programming becomes limited to ~ 3 sequences unless they are very short….need an alternative approach… Why?

Consider the 2 sequence comparison an o(mn) problem-order n2 i=01 Gap V c 32 j0123456 04-8-16-24 -3:8 8…44-4→12→-20→28 16-671→-9→17 241469 3222-14 30 0-30-22 133 48-38-30-15 23

Consider the 2 sequence comparison …..an O(mn) problem – order n2 i =0 1 2 3 4 5 j = Gap V D S C Y 0 0 4 -8 -4 -3 -8 -16 -24 -32 -40 -8 1 -8 4 -12 -20 -28 2 -16 -6 7 2 -1 -9 -17 3 -24 -14 1 -7 3 -6 9 4 -32 -22 -14 -30 3 0 5 -40 -22 -7 1 13 3 6 -48 -38 -30 -15 5 23

For 3 sequences. ARDE SHGLLENKLLGCDSMRWE GRDYKMALLEOWILGCD-MRWD SRDW--ALIEDCMV-CNEFRWD An o(mni problem! Consider sequences each 300 amino acids Uh oh !!! 2 sequences-( 300)2 our polynomail problem exponen 3 sequences-()3 but for sequences- 300)v

For 3 sequences…. ARDFSHGLLENKLLGCDSMRWE .::. .:::. .:::: :::. GRDYKMALLEQWILGCD-MRWD .::. ::.: .. :. .::: SRDW--ALIEDCMV-CNFFRWD An O(mnj) problem ! Consider sequences each 300 amino acids Uh Oh !!! 2 sequences – (300)2 Our polynomail problem 3 sequences – (300)3 Just became exponential! but for v sequences – (300)v

Consider pairwise alignments between 3 sequences Carillo and lipman-sum of Pairs method A-B-C Do we need to Score each node? moco o B-C A-B A-C Sequence A Get the multiple alignment score within the cubic lattice by Adding together the scores of the pairwise alignments

Consider pairwise alignments between 3 sequences Carillo and Lipman – Sum of Pairs method Sequence B CecneuqeS A-C A-B B-C A-B-C Do we need to Score each node? Sequence A Get the multiple alignment score within the cubic lattice by Adding together the scores of the pairwise alignments…

In practice, doesn't give optimal alignment. But were close Seems reasonable that the optimal alignment won't be far from the diagonal we were on, so we just set bounds on the location of the msa within the cube based on each pairwise-alignment Then just do dynamic programing within the volume defined by the pre-imposed bounds

In practice, doesn’t give optimal alignment…But we’re close! Seems reasonable that the optimal alignment won’t be far from the diagonal we were on…so we just set bounds on the location of the msa within the cube based on each pairwise-alignment. Then just do dynamic programing within the volume defined by the pre-imposed bounds

the volume is broken into polyhedra and the borders of the polyhedra are defined by paths through possible alignments

Still takes too long for more than three sequences. need a better way! Progressive Methods of Multiple Sequence Alignment Concept- simple: 1-Use DP to build pairwise alignments of most closely related sequences 2-Then progressively add less related sequences or groups of sequences

Still takes too long for more than three sequences…need a better way! • Progressive Methods of Multiple Sequence Alignment Concept – simple: 1-Use DP to build pairwise alignments of most closely related sequences 2- Then progressively add less related sequences or groups of sequences…

Clustalw Higgins and Sharp 1988 1-Do pairwise analysis of all the sequences (you choose similarity matrix) 2Use the alignment scores to make a phylogenetic tree 3- Align the sequences to each other guided by the phylogenetic relationships in the tree New features: Clustal E ClustalW (allows weights)L ClustalX(GUI-based Weighting is important to avoid biasing an alignment by many sequence Members that are closely related to each other evolutionarily

ClustalW Higgins and Sharp 1988 • 1- Do pairwise analysis of all the sequences (you choose similarity matrix). • 2- Use the alignment scores to make a phylogenetic tree. • 3- Align the sequences to each other guided by the phylogenetic relationships in the tree. New features: Clustal ⌦ClustalW (allows weights) ⌦ ClustalX (GUI-based Weighting is important to avoid biasing an alignment by many sequence Members that are closely related to each other evolutionarily!