This document discusses motifs, which are nucleotide or amino acid sequence patterns associated with biological functions. It defines motifs, patterns, and profiles. Motifs are conserved regions, patterns are qualitative expressions, and profiles are quantitative representations. It discusses tools for de novo prediction of motifs like MEME and resources for motif discovery. Finally, it provides examples of motifs, patterns, and building position specific scoring matrices from sample sequences.

1. Motif and Pattern Databases And
some practical approaches
Sucheta Tripathy
10/2/2016

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
• 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

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

6. 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

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. 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

11. MRLSFVPLLQLSRLVVSTQHSTKMSTVYRTCKMNEIALSLLAPTQPLDADQGVMSPMASSDQ
TTSIGDFRFLRTHHDKEERGLLVTSLTKGLAETSFPYR YTSMCATICSITHSRADAAPAKQAH

13. Prosite

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