Motif Discovery
Introduction
Pattern discovery algorithms are one way to uncover biological truths hidden in the massive amounts of sequence and gene expression data available. Sequence motifs are important in the understanding of protein structure and function, genetic regulation and proteinprotein, protein-nucleotide interactions.
Types of motifs and what they mean
Motifs in protein sequences Structure, function, evolution Motifs in DNA and RNA sequences Promoters, transcription factor binding sites, splicing signals
Motifs in Protein Sequences
The leucine zipper may explain how some eukaryotic gene regulatory proteins work. L-x(6)-L-x(6)-L-x(6)-L The leucine side chains extending from one alphahelix interact with those from a similar alpha helix of a second polypeptide, facilitating dimerization
Motifs in DNA Sequences
Motifs in DNA Sequences
Promoter regions, e.g. TATA box Transcription factor binding sites, e.g. Eve in Drosophila:
G-G-T-C-C-T-G-G
Cis-Regulatory regions
Motifs in RNA sequences
Human RNAsplice junctions sequence matrix
http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.html
Motifs in Protein Structures
Protein structure patterns can encode information about protein function. Structure motifs can be used to improve multiple alignments of protein sequences.
motif
motif
gap insert
BCTERIALGSPC1 Length of motif = 10 PCODE LNLSLTGVMA LNAQLNGVLA LNAQLNGVLA LNLSLTGVMV LNISLTGVLA LSLVLSGVVA GSQC_ERWCH GSPC_AERHY GSPC_AERSA GSPC_ERWCH GSPC_ERWCA GSPC_VIBCH Motif number = 1 ST 93 108 108 93 104 110 INT 93 108 108 93 104 110 General secretion pathway protein C motif I - 2
The Three Elements of Pattern Discovery
Pattern discovery requires: A pattern language This defines what kind of patterns you can find. An objective function This defines what makes a pattern "interesting". An algorithm This defines how to search among the possible patterns to find the "interesting" ones.

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