Understanding Motifs in Bioinformatics

Bioinformatics studies the patterns of sequences called motifs, which play significant roles in biological functions. Conserving information from DNA or proteins, motifs can be predicted de novo using various tools and strategies. Exploring these motifs aids in understanding regulatory elements and functional regions within biological sequences.

• Bioinformatics
• Motifs
• Sequence Patterns
• De Novo Prediction
• Regulatory Elements

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1. Subject Name Subject Code Semester : V Programme : Subject Name Bioinformatics Subject Code 17UMBE51 Semester : V Programme : B.Sc.Microbiology Bioinformatics 17UMBE51 B.Sc.Microbiology Dr Sajith Ahamed Assistant Professor Department of Microbiology HKRH College

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.

4. Motifs, profiles and patterns C[TA]TTG{X} C T T T G X Conserved region of a DNA or protein Motif Qualitative expression of a motif Pattern Regular Expression C[TA]TTG{X} C A T T G X [TA] C T T G any Quantitative expression of a motif Profile Position Specific Scoring Matrices (PSSMs) Weightmatrices

5. Motifs/Patterns N{P}[ST]{P} [FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY] [] -> or (Probability information is lost) {} -> Not () -> repeated ^ -> Beginning

7. 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)

8. 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

11. MRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQMRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQ TTSIGDFRFLRTHHDKEERGLLVTSLTKGLAETSFPYR YTSMCATICSITHSRADAAPAKQAH

13. Prosite

15. Scan this sequence and get me the motif ATGCGTCTCTCCTTCGTTCCACTACTGCAGCTCTCTCGTCTGGTCGTTAGCACACAACATAGTACGAAAATGA GCACAGTATACCGTACCTGCAAAATGAATGAAATAGCTCTCTCGTTGCTGGCGCCAACGCAGCCATTGGACG CTGACCAGGGTGTTATGTCACCGATGGCCTCATCAGACCAGACAACCTCAATTGG GAACCCACCACGATAAAGAAGAGCGGGGCTTGCTGGTTACCAGCCTCACAAAAGGTTTGGCTGAAACATCAT TTCCGTATCGATACACTTCGATGTGCGCAACTATTTGTTCAATTACGCATTCTCGGGCAGATGCTGCGCCTGC GAAGCAGGCGCACTA TGACTTTCGGTTCCTGA OR Build aPSSM ATGCGTCTCTC ATGCGTCTCTC ATGCGTCTATC ATGCCTCTGTC ATGCGTCTCTC