Motifs, patterns, profiles

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