FIMO and MAST are two applications in the MEME suites.

FIMO is looking for the best individual matches to motifs. MAST is looking for sequences the have the best overall match to a collection of motifs.

FIMO's task is simple: given a set of motifs and a database of sequences, compute the match score to each motif at each position in each sequence, and report all the motif matches that pass the p-value/q-value threshold.

MAST's algorithm is more complex. For each sequence it carries out an initial scoring that is quite similar to FIMO's. MAST then picks the best match for each motif in the sequence. The p-values for these top matches are multiplied together to create an overall score for the full sequence. MAST reports the sequences that have the most significant overall scores. Typically MAST would be used to look for regulatory regions in DNA, or structures in proteins, where several motifs might occur near each other.

-- Thanks to Charles for the explanation

FIMO is looking for the best individual matches to motifs. MAST is looking for sequences the have the best overall match to a collection of motifs.

FIMO's task is simple: given a set of motifs and a database of sequences, compute the match score to each motif at each position in each sequence, and report all the motif matches that pass the p-value/q-value threshold.

MAST's algorithm is more complex. For each sequence it carries out an initial scoring that is quite similar to FIMO's. MAST then picks the best match for each motif in the sequence. The p-values for these top matches are multiplied together to create an overall score for the full sequence. MAST reports the sequences that have the most significant overall scores. Typically MAST would be used to look for regulatory regions in DNA, or structures in proteins, where several motifs might occur near each other.

-- Thanks to Charles for the explanation

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