Motif discovery Tutorial 5

Motif discovery MEME Creates motif PSSM de-novo (unknown motif) MAST Searches for a PSSM in a DB TOMTOM Searches for a PSSM in motif DBs Agenda Cool story of the day: How NOT to be a bioinformatician

Motif – definition Motif a widespread pattern with a biological significance. Sequence motif PTB (RNA binding protein) UCUU CAP (DNA binding protein) TGTGAXXXXXXTCACAXT

Sequence motif – definition A000003/61/62/600 D03/62/6001/65/61/60 E004/ /6 G01/60011/30000 H01/ N Y /6 00..YDEEGGDAEE....YGEEGADYED....YDEEGADYEE....YNDEGDDYEE....YHDEGAADEE.. Motif a nucleotide or amino-acid sequence pattern that is widespread and has a biological significance PSSM - position-specific scoring matrix

Can we find motifs using multiple sequence alignment (MSA)? YES! NO Local multiple sequence alignment is a hard problem to solve

Motif search: from de-novo motifs to motif annotation gapped motifs Large DNA data

MEME

MEME – Multiple EM* for Motif finding Motif discovery from unaligned sequences - genomic or protein sequences Flexible model of motif presence (Motif can be absent in some sequences or appear several times in one sequence) *Expectation-maximization

MEME - Input Input file (fasta file) How many times in each sequence? How many motifs? How many sites? Range of motif lengths

MEME - Output Motif e- value

MEME – Sequence logo Motif length Number of appearnces Motif e- value A graphical representation of the sequence motif

MEME – Sequence logo High information content = High confidence The relative sizes of the letters indicates their frequency in the sequences The total height of the letters depicts the information content of the position, in bits of information.

Multilevel Consensus MEME – Sequence logo

Patterns can be presented as regular expressions [AG]-x-V-x(2)-{YW} [] - Either residue x - Any residue x(2) - Any residue in the next 2 positions {} - Any residue except these Examples: AYVACM, GGVGAA

Sequence names Position in sequence Strength of match Motif within sequence MEME – motif alignment

Overall strength of motif matches Motif location in the input sequence MEME – motif locations Sequence names

What can we do with motifs? MAST - Search for them in non annotated sequence databases (protein and DNA). TOMTOM - Find the protein which binds the DNA motifs.

MAST

Searches for motifs (one or more) in sequence databases: – Like BLAST but motifs for input – Similar to iterations of PSI-BLAST Profile defines strength of match – Multiple motif matches per sequence MEME uses MAST to summarize results: – Each MEME result is accompanied by the MAST result for searching the discovered motifs on the given sequences.

MAST - Input Input file (motifs) Database

If you wish to use motifs discovered by MEME

MAST - Output Input motifs Presence of the motifs in a given database

MAST – Output (another example, global view)

MAST – Output (another example, global view)

TOMTOM

Searches one or more query DNA motifs against one or more databases of target motifs, and reports for each query a list of target motifs, ranked by p-value. The output contains results for each query, in the order that the queries appear in the input file.

TOMTOM - Input Input motif Background frequencies Database

TOMTOM - Output Input motif Matching motifs

TOMTOM – Output Wrong input (RNA sequence of RNA binding protein NOVA1) “OK” results

MAST vs. TOMTOM MASTTOMTOM ComparisonProfile against DBProfile against Profile DBGeneral DBsKnown motif DBs

Cool Story of the day How NOT to be a bioinformatician