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Overview of Multiple Sequence Alignment Algorithms

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1 Overview of Multiple Sequence Alignment Algorithms
12/08/2016 Overview of Multiple Sequence Alignment Algorithms Yu He 04/13/2016 Adapted from Mingchao Xie and Julie Thompson multiple sequence alignment ppt online

2 Multiple sequence alignments
12/08/2016 Multiple sequence alignments Multiple Sequence Alignment (MSA) can be seen as a generalization of a Pairwise Sequence Alignment (PSA). Instead of aligning just two sequences, three or more sequences are aligned simultaneously. MSA is used for: Detection of conserved domains in a group of genes or proteins Construction of a phylogenetic tree Prediction of a protein structure Determination of a consensus sequence (e.g., transposons)

3 Multiple sequence alignments
12/08/2016 Multiple sequence alignments Example: part of an alignment of globin from 7 sequences H1 H2 H3 Symbol Meaning * Fully conserved : Conservation between groups of amino acids with strongly similar properties . Conservation between groups of amino acids with weakly similar properties Not conserved

4 Alignment algorithms Three types of algorithms:
12/08/2016 Alignment algorithms Three types of algorithms: 1. Progressive: Clustal W 2. Iterative: MUSCLE (multiple sequence alignment by log-expectation) 3. Hidden Markov models: HMMER Clustal Omega: Iterative progressive alignment using Hidden Markov models

5 Step 1 : Pairwise alignment of all sequences
Example : Alignment of 7 globins (Hbb_human, Hbb_horse, Hba_human, Hba_horse, Myg_phyca, Glb5_petma and Lgb2_lupla) Hbb_human 1 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST ... | |. |||.|| ||| ||| :|||||||||||||||||||||:|||||| Hbb_horse 2 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSN ... The alignment can be obtained with : - global or local methods - heuristic methods Hbb_human 1 LTPEEKSAVTALWGKV..NVDEVGGEALGRLLVVYPWTQRFFESFGDLST ... |.| :|. | | |||| . | | ||| |: . :| |. :| | ||| Hba_human 3 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF.DLS. ... Hba_human 3 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF.DLSH ... || :| | | | || | | ||| |: . :| |. :| | |||. Hbb_horse 2 LSGEEKAAVLALWDKVNEE..EVGGEALGRLLVVYPWTQRFFDSFGDLSN ... Adapted from Julie Thompson, IGBMC

6 Step 2 : Distance matrix construction
distance between two sequences = 1 - No. identical residues No. aligned residues Hbb_human Hbb_horse Hba_human Hba_horse Myg_phyca Glb5_petma Lgb2_lupla 1 - .17 - 2 3 4 5 6 7 1 2 3 4 5 6 7 Adapted from Julie Thompson, IGBMC

7 Step 3 : Guide tree construction
12/08/2016 Step 3 : Guide tree construction Guide tree Hbb_human Hbb_horse Myg_phyca Hba_human Glb5_petma Hba_horse Lgb2_lupla The time complexity for traditional approach is O(N^2). Cluster Omega uses a different method (mBed) to generate guide tree, which is (NlogN) much faster than Cluster W. UPGMA clustering method: - Join the two closest sequences, create consensus - Recalculate distances and join the two closest sequences or nodes - Step 2 is repeated until all sequences are joined Adapted from Julie Thompson, IGBMC

8 Step 4 : Progressive alignment
12/08/2016 Step 4 : Progressive alignment AVTALWGKVNVDEVGGEA AVTALWGKVNVDEVGGEA AVLALWDKVNEEEVGGEA AVLALWDKVNEEEVGGEA AVTALWGKVNV--DEVGGEA AVLALWDKVNE--EEVGGEA NVKAAWGKVGAHAGEYGAEA NVKAAWSKVGGHAGEYGAEA NVKAAWGKVGAHAGEYGAEA NVKAAWGKVGAHAGEYGAEA NVKAAWSKVGGHAGEYGAEA NVKAAWSKVGGHAGEYGAEA The sequences are aligned progressively (global or local algorithm) : - alignment of 2 sequences, create profile (consensus) - alignment of 1 sequence and a profile (group of sequences) - alignment of 2 profiles (groups of sequences) Cluster Omega uses HHalign to increase accuracy. Sequences alignment is converted to HMM, which then helps the alignment. Adapted from Julie Thompson, IGBMC

9 12/08/2016 Iterative alignment Iterative alignment refines an initial progressive multiple alignment by iteratively dividing the alignment into two profiles and realigning them. final alignment divide sequences Into two groups pairwise profile alignment yes profile 1 converged? refined alignment initial alignment Cluster Omega does iteration on both guide tree and hmm alignment. profile 2 no Adapted from Julie Thompson, IGBMC

10 Clustal Omega Navigate to:

11 Clustal Omega: setting up
12/08/2016 Clustal Omega: setting up Select sequence type Paste sequences into this box (you can also upload a file) The input for Clustal Omega is limited to a maximum of 2000 sequences. The default output format (ALN/Clustal format) truncates sequence identifiers to 30 characters. First 30 characters need to be unique.

12 Drosophila eyeless protein sequences
>Dmel MMLTTEHIMHGHPHSSVGQSTLFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPSNTTTAHLTLPPAASVVTSPANLSGQADRDDVQKRELQFSVEVSHTNSHDSTSDGNSEHNSSGDEDSQMRLRLKRKLQRNRTSFSNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSADTVDGSGRTSTANNPSGTTASSSVATSNNSTPGIVNSAINVAERTSSALVSNSLPEASNGPTVLGGEANTTHTSSESPPLQPAAPRLPLNSGFNTMYSSIPQPIATMAENYNSSLGSMTPSCLQQRDAYPYMFHDPLSLGSPYVSAHHRNTACNPSAAHQQPPQHGVYTNSSPMPSSNTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dgri MMLTTEHIMHGHPHSSVGVGMGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPGNTTTAHLALPPTPTAVPTNLSGQITRDEVQKRDLYPGDLSHPNSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKLRTQRRSVDNVGGTSGRTSTNNPSGSSVPTNATTANNSTSGIGTSAGSEGASTVHAGNNNPNETSNGPTILGGDASNVHSNSDSPPLQAVAPRLPLNTGFNTMYSSIPQPIATMAENYNSMTQSLSSMTPTCLQQRDSYPYMFHDPLSLGSPYAAHPRNTACNPAAAHQQPPQHGVYGNGSAVGTANTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dwil MMLTTEHIMHGHPHSSGMGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQSGGWAWYPSNTTTAHLALPPTPTAVPTPTNLSGQINRDDVQKRDLYPGDVSHPNSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKLRTQRRSVDNVGSSGRTSTNNNPNPSVTSVSTTAAPTGNGTPGLISSAAVNGSEESSSAIVGGNNTLADSPNGPTILGGEANTAHGNSESPPLHAVAPRLPLNTGFNTMYSSIPQPIATMAENYNSMTSTLGSMTPSCLQQRDSYPYMFHDPLSLGSPYAAHHRNTPCNPSAAHQQPPQHGGVYGNSAAMTSSNTGTGVISAGVSVPVQISTQNVSDLAGSNYWPRLQ >Dere MMLTTEHIMHGHPHSSVGQSTLFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPSNTTTPHLTLPPAASVVTSPANLSGQANRDDGQKRELQFSVEVSHTNSHDSTSDGNSEHNSSGDEDSQMRLRLKRKLQRNRTSFSNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSADTVDGSGRPSTSNNPSGTTASSSVATSNNSNPGIANSAIIVAERASSALISNSLPDASNGPTVLGGEANATHTSSESPPLQPATPRLPLNSGFNTMYSSIPQPIATMAENYNSSLGSMTPSCLQQRDAYPYMFHDPLSLGSPYVPAHHRNTACNPAAAHQQPPQHGVYTNSSAMPSSNTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dpse MMLTTEHIMHGHHPHSSVGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTSGWAWYPSNTTAHLALPPTPTALPTPTNLSGQINRDEVQKRDIYPGDVSHPSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSADNVGGSSGRASTNNQPSTAASSSVTPSSNSTPGIVSSAGNGIGSEGASSAIISNNTLPDTSNAPTVLGGDANATHTSSESPPLQAVAPRIPLNAGFNAMYSSIPQPIATMAENYNSMTSSLGSMTPTCLQQRDSYPYMFHDPLSLGSPYAPPHHRNAPCNPAAAHQQPPQHGVYGNSSSMTSNTGVISAGVSVPVQISTQNVSDLAGSNYWPRLQ

13 Clustal Omega results - alignments

14 Clustal Omega results – phylogenetic tree
The cladogram is a type of phylogenetic tree that allows you to visualize the evolutionary relationships among your sequences.

15 Clustal Omega results – result summary
12/08/2016 Clustal Omega results – result summary the students should include the collection of sequences that were used to produce the multiple sequence alignment in the appendix.

16 Use Jalview to visualize alignment

17 Alignment for eyeless protein in Drosophila species
12/08/2016 Alignment for eyeless protein in Drosophila species Clustal alignment with Drosophila species demonstrates conservation, but does not help you identify the important domains

18 Alignment for eyeless protein in broad range of species
12/08/2016 Alignment for eyeless protein in broad range of species Paired box domain Homeodomain The alignment with the broad range of species allows the identification of the highly conserved domains

19 12/08/2016 Conclusions Clustal Omega uses a modified iterative progressive alignment method and can align over 10,000 sequences quickly and accurately Clustal Omega is very useful for finding evidence of conserved function in DNA and protein sequences. But remember that sequence similarity does not always imply conserved function! Clustal Omega can be used to find promoters and other cis-regulatory elements.

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