FIMO: scan motif on a DNA sequence

Question

[mkh]

Hi All,

I am interested to understand how fimo (Find Individual Motif Occurrences ) works? In fact how PWM used as a prior information to find the probable motif occurrence in a DNA sequence? Unfortunately there is not enough description or computational method in FIMO original paper and I would be good if somebody can introduce me the original paper.

Thanks Morteza

[natasha.sernova]

This paper looks like an original one:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065696/

FIMO-description:

http://meme-suite.org/doc/fimo.html

MEME-suite (Motif-based sequence analysis tools) scheme:

http://meme-suite.org/

Some details about PWM:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436866/

See Background there

Answer 1

[natasha.sernova]

I just asked your question in google.com

math behind motif discovery AND PWM AND HMM model

I hope you will find enough math in two links I've found (they are at the bottom). If not, try to ask the same question in

www.ncbi.nlm.nih.gov or www.scholar.google.com

https://academic.oup.com/bioinformatics/article/31/16/2623/321303

https://www.researchgate.net/profile/Youlian_Pan/publication/258175982_Positional_weight_matrix_as_a_sequence_motif_detector/links/004635272c769374f5000000.pdf

Answer 2

[mkh]

Thanks .. It is very useful. But I meant the math behind motif discovery by having PWM and using HMM model.