Multiple Sequence Alignment Sequences > Yeast YOR020c > - PDF document

Multiple Sequence Alignment Sequences > Yeast YOR020c > Crypthecodinium cohnii mstllksaksivplmdrvlvqrikaqaktasglylpe matgiakrftplldrvlvqrlkpeaktasglflpesa knveklnqaevvavgpgftdangnkvvpqvkvgdqvl akapnyatvlavgpggrtrdgdilpmnvkvgdkvvvp ipqfggstiklgnddevilfrdaeilakiakd eyggmtlkfedeefqvfrdadimgilne > Neurospora crassa > Drosophila melanogaster mattvrsvksliplldrvlvqrvkaeaktasgiflpe maaaikkiipmldriliqraealtktkggivlpekav ssvkdlneakvlavgpgaldkdgkrlpmgvnagdrvl gkvlegtvlavgpgtrnastgnhipigvkegdrvllp ipqyggspvkvgeeeytlfrdseilakiae efggtkvnlegdqkelflfresdilakle > Aspergillus nidulans > Homo sapiens msllrnvknlaplldrvlvqrvkpeaktasgiflpes agqafrkflplfdrvlversaaetvtkggimlpeksq svkeqneakvlavgpgavdrngqripmgvaagdrvlv gkvlqatvvavgsgskgkggeiqpvsvkvgdkvllpe pqfggsplkigeeeyhlfrdseilakine yggtkvvlddkdyflfrdgxilgky > Schizosaccharomyces pombe (fission yeast) > Geobacillus stearothermophilus matklksaksivplldrilvqrikadtktasgiflpe vlkplgdrvvievieteektasgivlpdtakekpqeg ksveklsegrvisvgkggynkegklaqpsvavgdrvl rvvavgkgrvldsgervapevevgdriifskyagtev lpayggsnikvgeeeyslyrdhellaiike kydgkeylilresdilavig > Mortierella alpina > Mycobacterium tuberculosis masritkfsktivpmmdrvlvqrikpqqktasgiyip makvnikpledkilvqaneaetttasglvipdtakek ekaqealnegyvvavgkglttqegkvvpselaegdkv pqegtvvavgpgrwdedgekripldvaegdtviysky llppyggsvvkvdneelilfreseilakiq ggteikyngeeylilsardvlavvsk > Mus musculus (house mouse) magqafrkflllfdrvlversaaetvtkggimlpeks qgkvlqatvvavgsggkgksgeiepvsvkvgdkvllp eyggtkvvlddkdyflfrdsdilgkyvn 1

Multiple Sequence Alignment (MSA) Why MSA? • Proteins are often related to a larger group (i.e., a family) of proteins • Multiple sequence alignment is more sensitive than pairwise alignment for detecting homologs • MSAs can elucidate conserved residues, motifs, or other functional regions in a protein • MSA is critical for phylogenetic analysis – Selection of sequences – Multiple sequence alignment of sequences – Tree building – Tree evaluation 2

Pairwise Alignment 3-sequence Alignment AGA G T A AGT C C T TCC 0 0 0 0 A 0 5 0 0 G 0 0 10 4 0 5 4 6 A 3

Sequences > Yeast YOR020c > Crypthecodinium cohnii mstllksaksivplmdrvlvqrikaqaktasglylpe matgiakrftplldrvlvqrlkpeaktasglflpesa knveklnqaevvavgpgftdangnkvvpqvkvgdqvl akapnyatvlavgpggrtrdgdilpmnvkvgdkvvvp ipqfggstiklgnddevilfrdaeilakiakd eyggmtlkfedeefqvfrdadimgilne > Neurospora crassa > Drosophila melanogaster mattvrsvksliplldrvlvqrvkaeaktasgiflpe maaaikkiipmldriliqraealtktkggivlpekav ssvkdlneakvlavgpgaldkdgkrlpmgvnagdrvl gkvlegtvlavgpgtrnastgnhipigvkegdrvllp ipqyggspvkvgeeeytlfrdseilakiae efggtkvnlegdqkelflfresdilakle > Aspergillus nidulans > Homo sapiens msllrnvknlaplldrvlvqrvkpeaktasgiflpes agqafrkflplfdrvlversaaetvtkggimlpeksq svkeqneakvlavgpgavdrngqripmgvaagdrvlv gkvlqatvvavgsgskgkggeiqpvsvkvgdkvllpe pqfggsplkigeeeyhlfrdseilakine yggtkvvlddkdyflfrdgxilgky > Schizosaccharomyces pombe (fission yeast) > Geobacillus stearothermophilus matklksaksivplldrilvqrikadtktasgiflpe vlkplgdrvvievieteektasgivlpdtakekpqeg ksveklsegrvisvgkggynkegklaqpsvavgdrvl rvvavgkgrvldsgervapevevgdriifskyagtev lpayggsnikvgeeeyslyrdhellaiike kydgkeylilresdilavig > Mortierella alpina > Mycobacterium tuberculosis masritkfsktivpmmdrvlvqrikpqqktasgiyip makvnikpledkilvqaneaetttasglvipdtakek ekaqealnegyvvavgkglttqegkvvpselaegdkv pqegtvvavgpgrwdedgekripldvaegdtviysky llppyggsvvkvdneelilfreseilakiq ggteikyngeeylilsardvlavvsk > Mus musculus (house mouse) magqafrkflllfdrvlversaaetvtkggimlpeks qgkvlqatvvavgsggkgksgeiepvsvkvgdkvllp eyggtkvvlddkdyflfrdsdilgkyvn Multiple Sequence Alignment 4

Pairwise Alignment Scores Crypthecodinium Schizoscchrmycs Mycobacterium Geobacillus Neurospora Aspergillus Mortierella Drosophila Homo Yeast Mus 49 46 78 45 55 54 44 38 37 42 Yeast 52 41 40 43 46 44 41 39 43 Neurospora 43 48 45 45 40 40 38 39 Aspergillus 42 53 55 41 41 40 40 Schizosaccharomyces 43 46 40 43 38 39 Mortierella 61 43 34 36 45 Crypthecodinium 49 42 36 49 Drosophila 37 32 93 Homo 59 38 Geobacillus 32 Mycobacterium Mus Guide Tree Neurospora Aspergillus Yeast Schizosaccharomyces Crypthecodinium Drosophila Geobacillus Mycobacterium Mortierella Homo Mus 5

Constructing a Guide Tree • Unweighted pair group method with arithmetic mean (UPGMA) • Neighbor joining (NJ) Unweighted Pair Group Method with Arithmetic mean (UPGMA) • Assume each organism is its own group • Repeat the following step – Merge together the two closest groups 6

Unweighted Pair Group Method with Arithmetic mean (UPGMA) Neurospora Schizosaccharomyces Aspergillus Yeast Crypthecodinium Mycobacterium Drosophila Geobacillus Mus Crypthecodinium Mycobacterium Neurospora Aspergillus Yeast Schizosaccharomyces Drosophila Geobacillus Mortierella Homo Mus Homo Mortierella Unweighted Pair Group Method with Arithmetic mean (UPGMA) Neurospora Schizosaccharomyces Aspergillus Yeast Crypthecodinium Mycobacterium Drosophila Geobacillus Mus Neurospora Aspergillus Crypthecodinium Drosophila Mycobacterium Mortierella Yeast Schizosaccharomyces Geobacillus Homo Mus Homo Mortierella 7

Neurospora Aspergillus Yeast Schizosaccharomyces Crypthecodinium Unweighted Pair Group Method with Drosophila Geobacillus Mycobacterium Arithmetic mean (UPGMA) Mortierella Neurospora Homo Aspergillus Mus Yeast Schizosaccharomyces Guide Tree Crypthecodinium Mycobacterium Drosophila Geobacillus Geobacillus Aspergillus Mycobacterium Mortierella Mortierella Neurospora Homo Mus Drosophila Yeast Schizosaccharomyces Homo Mus Crypthecodinium 12

Neighbor Joining (NJ) • Generate full tree with starlike structure • Repeat the following step – Connect two closest groups (i.e., neighbors) through a single node Neighbor Joining Geobacillus Mycobacterium Yeast Mortierella Schizosaccharomyces Mus Crypthecodinium Homo Drosophila Neurospora Aspergillus 13

Neighbor Joining Geobacillus Mycobacterium Yeast Mortierella Schizosaccharomyces Mus Crypthecodinium Homo Drosophila Neurospora Aspergillus Neighbor Joining Geobacillus Mycobacterium Yeast Mortierella Schizosaccharomyces Mus Crypthecodinium Homo Drosophila Neurospora Aspergillus 14

Multiple Sequence Alignment Sequences > Yeast YOR020c > - PDF document

Multiple Sequence Alignment Sequences > Yeast YOR020c > Crypthecodinium cohnii mstllksaksivplmdrvlvqrikaqaktasglylpe matgiakrftplldrvlvqrlkpeaktasglflpesa knveklnqaevvavgpgftdangnkvvpqvkvgdqvl akapnyatvlavgpggrtrdgdilpmnvkvgdkvvvp

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