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Motif andpatterndatabase

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Motifs, patterns, profiles

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Motif andpatterndatabase

  1. 1. Motif and Pattern Databases And some practical approaches Sucheta Tripathy 10/2/2016
  2. 2. Motifs • Defined as a nucleotide or amino acid sequence pattern that is widespread and is associated with a biological function. – A sequence motif = A structural Motif. – A sequence motif residing in the coding region may encode a structural motif. – Non-coding nucleotide motifs may have regulatory role. May have recognition sites for DNA binding proteins.
  3. 3. Motifs, profiles and patterns • Conserved region of a DNA or protein – Motif • Qualitative expression of a motif – Pattern – Regular Expression – C[TA]TTG{X} • Quantitative expression of a motif – Profile – Position Specific Scoring Matrices (PSSMs) – Weight matrices
  4. 4. Motifs/Patterns N{P}[ST]{P} [FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY] [] -> or (Probability information is lost) {} -> Not () -> repeated ^ -> Beginning
  5. 5. Profiles • Quantitative representation. • More useful for training dataset. TCTAGAAGATGGCAGTGGCGAAGA TCTAGAAAATGACAGTGGCGAAGA TCTAGAAAATGGCAGTAGCGAAGA TCTACTAAATGA TAGTAGCGAAGA A 0,0,0,100 ,0, 75,100, 75 ATG T 100,0,100,0,0, 25, 0, 0 ATG G 0, 0, 0, 0, 75 ,0, 0, 25 ATG C 0,100,0,0, 25 ,0, 0, 0 ATG
  6. 6. De novo prediction of Motifs • MEME; EXTREME; AlignAce, Amadeus, CisModule, FIRE, Gibbs Motif Sampler, PhyloGibbs, SeSiMCMC, ChIPMunk and Weeder. SCOPE, MotifVoter, and Mprofiler MEME (Multiple Expectation Maximization for Motif Elicitation)
  7. 7. Figure 3. Resources MacIsaac KD, Fraenkel E (2006) Practical Strategies for Discovering Regulatory DNA Sequence Motifs. PLoS Comput Biol 2(4): e36. doi:10.1371/journal.pcbi.0020036 http://journals.plos.org/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.0020036
  8. 8. MRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQ TTSIGDFRFLRTHHDKEERGLLVTSLTKGLAETSFPYR YTSMCATICSITHSRADAAPAKQAH
  9. 9. Prosite
  10. 10. ATGCGTCTCTCCTTCGTTCCACTACTGCAGCTCTCTCGTCTGGTCGTTAGCACACAACATAGTACGAAAATGA GCACAGTATACCGTACCTGCAAAATGAATGAAATAGCTCTCTCGTTGCTGGCGCCAACGCAGCCATTGGACG CTGACCAGGGTGTTATGTCACCGATGGCCTCATCAGACCAGACAACCTCAATTGG TGACTTTCGGTTCCTGA GAACCCACCACGATAAAGAAGAGCGGGGCTTGCTGGTTACCAGCCTCACAAAAGGTTTGGCTGAAACATCAT TTCCGTATCGATACACTTCGATGTGCGCAACTATTTGTTCAATTACGCATTCTCGGGCAGATGCTGCGCCTGC GAAGCAGGCGCACTA Scan this sequence and get me the motif OR Build a PSSM ATGCGTCTCTC ATGCCTCTGTC ATGCGTCTCTC ATGCGTCTCTC ATGCGTCTATC

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