TOMTOM

[jasdeep kaur]

Hi

is it possible to do differential motif search in meme suite ?

For example: a SNP sequence

                        ref allele: CCAGTTCTTTTAGCC                                     ​

                       alt allele : CCAGTTCATTTAGCC  

thanks

jasdeep

[cegrant]

I'm afraid your question is not entirely clear. What do you mean by differential motif search?

Also, note that Tomtom is not a motif search tool, rather it performs motif comparisons, identifying motifs that are similar to each other. Internally motifs are represented as position weight matrices (PWM), not as sequences or regular expressions. Since your two alleles differ only at a single position Tomtom would score them as highly similar to each other.

[jasdeep kaur]

Hi,

I apologize. I'll put my questions separately and are entirely unrelated. 

1)I have to do motif search in a Single nucleotide polymorphism sequence. lets take an example sequence as pasted above. Does MEME suite has the functionality to do such kind of motif search ?

2) I have a motif which binds to one allele  e.g. to this allele alt allele : CCAGTTCATTTAGCC  and I want to force check its binding for another allele that is  ref allele: CCAGTTCTTTTAGCC .

Thanks

jasdeep

[cegrant]

1) MEME doesn't do motif search, it does motif discovery. That is, you give it a collection of sequences that you think contain a common motif, but you don't know what the motif is. MEME then returns the most plausible candidates for the motif. FIMO does motif search, that is, you provide a motif and collection of sequences and FIMO returns the locations in the sequences that match the given motif, with a match score p-value higher then a user chosen threshold. I'm afraid I'm still not entirely sure what you mean by "I have to do motif search in a Single nucleotide polymorphism sequence". The key point about motif search is that it doesn't require an exact match at every position. Rather is compares  each point in the sequence with the position weight matrix for the motif. If you want to search for matches to either CCAGTTCTTTTAGCC or CCAGTTCATTTAGCC, you could type that into FIMO as a motif as CCAGTTC[AT]TTTAGCC, which would allow either A or T at the 8th position.

2) None of the MEME Suite tools directly evaluate transcription factor binding, but the FIMO match score  can be used as a proxy to compare binding for a single motif at two positions. The higher the score,  presumably the stronger the binding. However, the scores are not calibrated, so you can't compare binding of two different motifs. Of course the accuracy of the FIMO match scores depends on the accuracy of the motif you search with.