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Multiple sequence alignments with Clustal Omega Yu He 04/13/2016 Adapted from Mingchao Xie and Julie Thompson multiple sequence alignment ppt online.

Published byMargaret Davis Modified over 8 years ago

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Presentation on theme: "Multiple sequence alignments with Clustal Omega Yu He 04/13/2016 Adapted from Mingchao Xie and Julie Thompson multiple sequence alignment ppt online."— Presentation transcript:

1 Multiple sequence alignments with Clustal Omega Yu He 04/13/2016 Adapted from Mingchao Xie and Julie Thompson multiple sequence alignment ppt online

2 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 Example: part of an alignment of globin from 7 sequences SymbolMeaning *Fully conserved :Conservation between groups of amino acids with strongly similar properties.Conservation between groups of amino acids with weakly similar properties Not conserved H1 H2 H3

4 Alignment 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 Three types of algorithms:

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

6 -.17-.59.60-.59.59.13-.77.77.75.75-.81.82.73.74.80-.87.86.86.88.93.90- Hbb_human Hbb_horse Hba_human Hba_horse Myg_phyca Glb5_petma Lgb2_lupla 1 2 3 4 5 6 7 1234567 Step 2 : Distance matrix construction distance between two sequences = 1 - No. identical residues No. aligned residues Adapted from Julie Thompson, IGBMC

7 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 Hbb_human Hbb_horse Hba_human Hba_horse Myg_phyca Glb5_petma Lgb2_lupla Guide tree Step 3 : Guide tree construction Adapted from Julie Thompson, IGBMC

8 Step 4 : Progressive alignment 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) Adapted from Julie Thompson, IGBMC AVTALWGKVNVDEVGGEA AVLALWDKVNEEEVGGEA NVKAAWGKVGAHAGEYGAEA NVKAAWSKVGGHAGEYGAEA AVTALWGKVNVDEVGGEA AVLALWDKVNEEEVGGEA NVKAAWGKVGAHAGEYGAEA NVKAAWSKVGGHAGEYGAEA AVTALWGKVNV--DEVGGEA AVLALWDKVNE--EEVGGEA NVKAAWGKVGAHAGEYGAEA NVKAAWSKVGGHAGEYGAEA

9 Iterative alignment initial alignment divide sequences Into two groups profile 1 profile 2 pairwise profile alignment refined alignment converged? no Iterative alignment refines an initial progressive multiple alignment by iteratively dividing the alignment into two profiles and realigning them. Adapted from Julie Thompson, IGBMC yes final alignment

10 Clustal Omega Navigate to: http://www.ebi.ac.uk/Tools/msa/http://www.ebi.ac.uk/Tools/msa/

11 Clustal Omega: setting up Select sequence type Paste sequences into this box (you can also upload a file)

12 Eyeless protein in Drosophila species >Dmel MMLTTEHIMHGHPHSSVGQSTLFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIA DYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPSNTTTAHLTLPPAASVVTSPANLSGQADRDDVQK RELQFSVEVSHTNSHDSTSDGNSEHNSSGDEDSQMRLRLKRKLQRNRTSFSNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSA DTVDGSGRTSTANNPSGTTASSSVATSNNSTPGIVNSAINVAERTSSALVSNSLPEASNGPTVLGGEANTTHTSSESPPLQPAAPRLPLNSGFNTMYSSIPQPIATMAENYNS SLGSMTPSCLQQRDAYPYMFHDPLSLGSPYVSAHHRNTACNPSAAHQQPPQHGVYTNSSPMPSSNTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dgri MMLTTEHIMHGHPHSSVGVGMGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPV VQKIADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPGNTTTAHLALPPTPTAVPTNLSGQITRDEV QKRDLYPGDLSHPNSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKLRTQRRSV DNVGGTSGRTSTNNPSGSSVPTNATTANNSTSGIGTSAGSEGASTVHAGNNNPNETSNGPTILGGDASNVHSNSDSPPLQAVAPRLPLNTGFNTMYSSIPQPIATMAENY NSMTQSLSSMTPTCLQQRDSYPYMFHDPLSLGSPYAAHPRNTACNPAAAHQQPPQHGVYGNGSAVGTANTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dwil MMLTTEHIMHGHPHSSGMGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQK IADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQSGGWAWYPSNTTTAHLALPPTPTAVPTPTNLSGQINRDDVQK RDLYPGDVSHPNSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKLRTQRRSVD NVGSSGRTSTNNNPNPSVTSVSTTAAPTGNGTPGLISSAAVNGSEESSSAIVGGNNTLADSPNGPTILGGEANTAHGNSESPPLHAVAPRLPLNTGFNTMYSSIPQPIATMA ENYNSMTSTLGSMTPSCLQQRDSYPYMFHDPLSLGSPYAAHHRNTPCNPSAAHQQPPQHGGVYGNSAAMTSSNTGTGVISAGVSVPVQISTQNVSDLAGSNYWPRLQ >Dere MMLTTEHIMHGHPHSSVGQSTLFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKIA DYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTGGWAWYPSNTTTPHLTLPPAASVVTSPANLSGQANRDDGQK RELQFSVEVSHTNSHDSTSDGNSEHNSSGDEDSQMRLRLKRKLQRNRTSFSNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSA DTVDGSGRPSTSNNPSGTTASSSVATSNNSNPGIANSAIIVAERASSALISNSLPDASNGPTVLGGEANATHTSSESPPLQPATPRLPLNSGFNTMYSSIPQPIATMAENYNSS LGSMTPSCLQQRDAYPYMFHDPLSLGSPYVPAHHRNTACNPAAAHQQPPQHGVYTNSSAMPSSNTGVISAGVSVPVQISTQNVSDLTGSNYWPRLQ >Dpse MMLTTEHIMHGHHPHSSVGQSALFGCSTAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATTPVVQKI ADYKRECPSIFAWEIRDRLLSEQVCNSDNIPSVSSINRVLRNLASQKEQQAQQQNESVYEKLRMFNGQTSGWAWYPSNTTAHLALPPTPTALPTPTNLSGQINRDEVQKRD IYPGDVSHPSHESTSDGNSDHNSSGDEDSQMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKMRTQRRSADNVG GSSGRASTNNQPSTAASSSVTPSSNSTPGIVSSAGNGIGSEGASSAIISNNTLPDTSNAPTVLGGDANATHTSSESPPLQAVAPRIPLNAGFNAMYSSIPQPIATMAENYNSM TSSLGSMTPTCLQQRDSYPYMFHDPLSLGSPYAPPHHRNAPCNPAAAHQQPPQHGVYGNSSSMTSNTGVISAGVSVPVQISTQNVSDLAGSNYWPRLQ

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

16 Use Jalview to visualize alignment

17 Alignment for Eyeless protein in Drosophila species

18 Alignment for Eyeless protein in broad range of species Paired box domain Homeodomain

19 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. Conclusions

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