11 Multiple Sequence Alignment 2

11 Multiple Sequence Alignment 2 - 1 Introduction to...

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1 Introduction to Bioinformatics/ Elements of Bioinformatics Multiple sequence alignment (II)
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2 References • Mount D.W. (2004) Bioinformatics: Sequence and Genome Analysis. 2 nd ed. Cold Spring Harbor Lab. Press, N.Y. Chapter 5 . • Attwood, T.K. (2000) The quest to deduce protein function from sequence: The role of pattern databases. International Journal of Biochemistry and Cell Biology 32: 139-55.
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3 Sequence patterns • Conserved sequence regions (motifs) from global or local multiple alignments: – Consensus sequences – Regular expression (PROSITE) patterns – PSSM (position-specific scoring matrix, ungapped alignment) – Profiles (may contain gaps) – Hidden Markov models
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4 Consensus sequences Consensus IUPAC
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5 Symbols for DNA Symbols Meaning A Adenine G Guanine C Cytosine T Thymine R A or G (puRine) Y C or T (pYrimidine) W A or T (Weak bonds) S C or G (Strong bonds) M A or C (Amino) K G or T (Keto) B C or G or T (Not A) H A or C or T (Not G) D A or G or T (Not C) V A or C or G (Not T) N G or A or T or C (Any)
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6 Reference: Attwood, T.K. (1997) Exploring the language of bioinformatics. In Oxford Dictionary of Biochemistry and Molecular Biology . pp 715-723. Oxford University Press Protein family databases derived from multiple sequence alignment
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7 Protein Primary source Information (on functional Family sites or domains) Database PROSITE SwissProt Regular expression (patterns) PRINTS SwissProt/ Aligned motifs TrEMBL (fingerprints) BLOCKS InterPro/ Aligned motifs PRINTS (blocks) Profiles SwissProt Weighted matrices (PROSITE) (profiles) Pfam SwissProt Hidden Markov TrEMBL Models (HMMs)
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8 Protein family databases • PROSITE database: – Protein families characterized by single most conserved motif in known homologues – Conserved motifs encode key biological functions – Motifs are encoded as regular expressions (patterns)
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Construction of a PROSITE pattern E T D I K I M E R V E V E V K M M E R V E K E I K I M E K V E S S V K M M E K V E T T K K I M E R V
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11 Multiple Sequence Alignment 2 - 1 Introduction to...

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