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Multiple Sequence Alignment Slides

Multiple Sequence Alignment Slides - Computational Biology...

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- p.1/49 Computational Biology Multiple Sequence Alignment (MSA)
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- p.2/49 Definition of a Global MSA Generalization of a pairwise alignment to more than 2 sequences Insert spaces into each of the k strings such that resulting strings have all the same length Modified strings are arrayed in k rows and l columns where each character and space of each string is in a unique column.
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- p.3/49 Example: Sequences from Triosephosphate Isomerase R i c e : CNGTTDQVDKIVKILNEGQIASTDVVEVVV...KGVSA M o s q u i t o : MNGDKASIADLCKVLTTGPLNADTEVVVGC...ISP H u m a n : MNGRKQSLGELIGTLNAAKVPADTEVVCAP...ISP M o n k e y : MNGRKQNLGELIGTLNAAKVPADTEVVCAP...ISP as a result we get: 1 CNGTTDQVDKIVKILNEGQIASTDVVEVVV...VSA 4 MNGRKQNLGELIGTLNAAKVPAD__TEVVC...ISP 3 MNGRKQSLGELIGTLNAAKVPAD__TEVVC...ISP 2 M N G D K A S I A D L C K V L T T G P L N A D T E V V V . . . I S P __
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- p.4/49 MSA inverse to PSA In database searches, pairwise alignment is used to identify previously unknown biological relationship based on sequence similarity In MSA we are doing the inverse problem, based on known biological relationships between sequences, we want to identify unknown conserved subpatterns
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- p.5/49 Biological Relevance of MSA High sequence similarity implies high functional or structural similarity Sequences with functional or structural similarity can differ a lot in their sequences -~  Pairwise alignments cannot detect the latter cases
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- p.6/49 Biological Relevance of MSA II Example: Hemoglobin 4 chains of about 140 AA each contained in organisms as diverse as mammals and insects about 100 AA-mutations in each of the chains since divergence of insects and invertebrates
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- p.7/49 E x a mp le lengths=141,141 simil=385.3, PAM_dist=105, identity=40.4% ID=HBA HUMAN AC=P01922; DE=Hemoglobin alpha chain. OS=Homo sapiens _ (Human), Pan troglodytes (Chimpanzee), and Pan paniscus (Pygmy chimpanzee) (Bonobo). OC=Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. KW=Heme; Oxygen transport; Transport; Erythrocyte; Disease mutation; Polymorphism; Acetylation; 3D-structure. RES=1.5 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAH |||| ||:.|..|||:|||::|: .|...|!!|:.||.:..| |.:|:|||:|.!.|||!||.|:.|::... VLSPFDKAGVIKAWGQVGANTGQGDAMGAEKLFFDFPRSAGYNPALDVSHGAAYITGHGRKVLDTATDTYKM VDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR !|. |.:!.:||| :...|.|.|.:!|.|:. !.|.!|:. ..|:|..|...||.||||...!!| .|| IDAGPASMCSLSDGQPRGLVVGPFKYKQLTTEIAVPMATCEADELTQGVEGMLDTFLASPIEIITLSYR
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- p.8/49 Bottom line Structurally and functionally conserved molecules can differ in sequence ~ pairwise alignments will not reveal conserved patterns Other extreme: Comparison of 2 sequences with very high similarity ~ important patterns lost in high similarity MSA: compare multiple related sequences simultaneously to reveal critical patterns
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- p.9/49 Graphical explanation too similar
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- p.10/49 Use of MSA MSA are used in the following 3 kinds of inquiries 1.representation of protein families 2.identification of conserved features in DNA or proteins 3.deduction of evolutionary history (phylogenetic trees) ~ tasks are interrelated, all assume that common function or structure results from common evolu- tionary history
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